It would be kind of silly if you couldn't group up devices like that. If you think about it, modern networks work very much like this. Take a modern-day setup. We have companies with servers that all slave a number of computers to themselves. Those computers, in turn, will slave other devices (such as flash drives, mice, keyboards, monitors, ect.)
Your rational is correct. You can, indeed, create groups of devices, slave them to a commlink, and then have the decker slave the commlinks to himself. This creates a mobile PAN (personal area network) mesh that the decker can more easily police and protect, since he's the first thing an enemy hacker has to get through. There are, of course, problems with this setup.
The biggest flaw to this setup is what happens when someone DOES make it through your detection and firewall unchecked? The answer? They now have EVERY piece of hardware your entire team owns at their fingertips. And until you can get them out of your node, they can choose to screw with any of the devices. Normally, if they want to hack the street sam, they'd need to be within range and hack their commlink separately. It's easier, but that's multiple points of failure, since the enemy hacker can't get to anyone else on your team through the sam. With you protecting the group, you're more likely to catch any intrusion, but if you fail, the enemy hacker now has three marks on your entire team and hilarity can ensue (read: bad things for your team).
Generally, you want to protect all of your party members and slave all of their devices to your deck. Period. There is no reason NOT to do this, honestly. The chances that you'll miss a hacker in your system are pretty low anyways, and even if you do miss them, rebooting your deck will sever the connection and erase the hacker's marks on your deck, forcing the enemy hacker to have to start again on someone else's device.
When questions come up about how much detail to plan for when prepping for a campaign/session etc, one of the answers I tend to agree with is that you only do as much as the players are going to see/experience. There's no point in having a detailed history of some far off land if it is never going to come up.
To a certain extent the same applies here. Shadowrun's tropes tend towards having these complex, multi-layered schemes and plots, with various rival factions backstabbing each other and noone trusting anybody. The problem is, as a GM you can come up with these clever stories, but unless the players run into the details somehow then a large part of the effort is wasted. (A slight caveat to this is that knowing this information can cover you if your group is prone to going off in unexpected directions, as the detail can help you improvise on the fly).
If you assume that Mr. Johnson is as smart as you say, then the PCs are going to have to work to get the information on the complexity, and this leads to one of the key things – you need to give them a reason to dig further. There needs to be some sort of motivation for the group to start peeling back the layers of the plots to reveal just how clever/convoluted everything is.
Assuming that you think the PCs care, then you need to leave a trail of clues. As you say, Mr Johnson is too clever to do anything really stupid, which cuts out many of the obvious choices, but there are still as many options here as your fevered imagination can come up with.
For example, perhaps the PCs overhear snippets of conversation with other involved parties, or come across news stories or other media that make oblique references to characters/places etc the PCs are encountering. The key thing here is to be subtle and not spell the connections out too obviously. Assuming that you've laid the ground work and the players/PCs have the appropriate motivation, let them join the dots and fill in the gaps. This can lead to some fertile ground for further adventures as the group of runners plots how to extract proof of what is going on. Things can be especially fun if/when they make incorrect assumptions.
The key thing through all this though is not to force it. If you want to stay true to the motivations and intelligence of a typical Mr Johnson then you're absolutely correct, they wouldn't be so stupid as to leave details of their plans lying around to be found. However, all people make mistakes however small, and with the number of parties that are involved in your typical Shadowrun adventure, there is massive scope for information leaks in various forms that the PCs can stumble on. Don't explain everything, and make the PCs work and leave plenty of room for assumptions as to what is going on. A typical group of Shadowrunners are unlikely to ever have a complete picture, and that is fine.
It can be really difficult for a GM who has put such a huge amount of work into a clever plot not to want make it absolutely clear to the players how good it is, but resist this urge. A bit of confusion is a wonderful thing to prompt a healthy amount of paranoia, and then you sit back and smile to yourself as the players gradually realise just how deep the rabbit hole really goes and how far they are in over their heads.
Best Answer
This answer comes down primarily to "What about..."
Noise?
This is the biggest one
Why is your Decker not in the field? The ability to hack the stuff in the run location requires that he get in close physical proximity to it. That's how the SR5 Matrix works. The whole "I'm a Decker who sits and home and does all my work remotely" doesn't fly in SR5, because of the Noise mechanics. The further you are from something and the more stuff is in between you and the thing you're trying to hack--the bigger penalties you take to trying to hack it. Any site worth their salt knows this and would set up countermeasures (like walls, Em-blocking paint, landscaping, a Faraday Cage, or just by putting important things away from the exterior of the building) that prevent someone from hacking into their stuff from outside the building.
In short...in SR5, a Decker can do some work remote--such as setting up fake IDs or getting blueprints and so on...but they can't mess with the cameras, control locks, disable security systems, shut the alarm off, break into a computer for a datasteal, or anything else like it without being with the team breaking into the building.
And that's not to mention that some security systems, data repos, etc. are offline and thus cannot be accessed without a direct physical connection to that thing.
And no, 'routing' through a friend's commlink doesn't work, because you get all that Noise trying to connect to them, too.
Tactical Support?
Does your Decker not realize how useful they are in dealing with other sorts of obstacles?
DataSteals?
Probably the most common job in the SR world is the datasteal...get in, get your Decker close to a secured data repository, then let them hack into it and steal it. Because of the Noise issues mentioned above, the Decker must by with the team because otherwise he would be operating at something like a -200 dice pool.
Other Skills
Deckers, by necessity, have high Logic. This also makes them well-suited to be good at any of the Mechanic skills, as well as Medicine and Demolitions. Any of those skills can be useful on the actual run...especially if no one on the team has those skills.
The ability to cleanly sabotage a piece of tech requires that you be able to understand that tech and know how it works...Smashy the Street Samurai can break the thing, but sabotage that makes it look like it failed on its own requires skill in working on the thing you're trying to sabotage.
Summary
This doesn't seem like a DM-style issue to me. If I had to guess, you're ignoring the Noise rules, and that's what is causing this issue...if the Decker doesn't have to go with the team to do their job, then of course they are going to do it all remotely then sit safely at home. That's kind of the whole point of the Noise rules--force the Decker to actually go on the run with the rest of the team