The package is a Faraday cage with some magic to make it invisible. The former point is there to stop scans. The latter to stop magical examinations. When opened, the little transmitted inside it goes beep and tells Mrs Drone to release Mr Missile to come to the rescue. If the PCs open it before hand, then the missile goes to where they are. This gives the PCs some change to flee before the missile arrives. Thus you have no need to have a super stealth bomb that is shoddy and does not work. In addition, it should scare the PCs that the opposition has access to military drones.
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
Let them
No seriously, let them.
They want to keep the McGuffin of doom, the schematics to the bank that the Johnson asked them to get, the sacred Rhino of the city?
Let them keep them.
They're seriously writing plot for you right here, don't speak to them as a GM saying "If you do that, X..." they're experienced runners now; this is fine at the start of games when players are learning systems, but when they know the world more, they've done a few runs - they need to expand out and be let free from the cotton wool of GM warnings.
Give them an OOC 'the talk' before the next game; "You're experienced runners now, what you do is up to you, what happens will happen as a consequence of that, so think carefully about stuff before you do it."
You can still give them warnings that their characters know about, if they wouldn't think of... "Hey Street sam, you know for a fact from your street contacts that holding onto a jacket from the DOOM X bikers gang is a way to get the gang hunting you down. Just so you know."
Why letting players keep stuff is great for your game
Rep is great, it gets you off the hook; but like stocks and shares, it can go up and down. If they start doing Jobs for their Johnson and not finishing as required, then the next one will be a bit harder to do, the pay less... and so on.
Let them keep the stuff. Really.
Don't say anything. Well maybe just...
Player: Screw the Johnson, let's keep this Sabre-X missile launcher, it's awesome.
Other Players: Hell yeah!
GM: ~smiles to themself~ ~writes something down~
They'll learn to fear that smile ;)