It should be fine, as long as time allows.
Nothing in the rules says that a long rest cannot immediately follow a short rest. In this case, what the characters are doing during those rests are very different.
Indeed, a short rest and a long rest are what many real-life people do before bed: an hour or so of non-strenuous activity, like reading, and then going to sleep. It's not a stretch to say that a D&D character can't spend an hour studying their magical item, and then go to sleep.
The only time where that might be a problem is if the characters don't have the full 9 hours.
Different things are happening during the two rests.
What's really key here is that the activities during the two rests are different. In the short rest portion, the character is studying the magic item, meditating on it, or whatever is required for attunement. In the long rest portion, the character is doing something else, such as sleeping. The attunement process is still active work, just not active relative to adventuring.
I think that this distinction is why attunement is limited to short rests, and why a character should be able to do chain them together.
In the case of a specific story, you have to ask what makes sense.
In terms of the mandatory 24-hour waiting period between long rests...players can always wander off and go burn the rest of the day foraging, chatting, and otherwise being idle. If they elect to take a long-rest part way through a 'dungeon crawl' make sure you consider exactly what that means for them.
For the number of encounters they can handle in a day, per the DMG, it recommends:
most adventuring parties can handle about six to eight medium or hard encounters in a day. If the adventure had more easy encounters, the adventurers can get through more. If it has more deadly encounters, they can handle fewer. (DMG84)
Remember that this is a guideline. And guidelines tend to be broken on occasion.
So, for the specific case of a published adventure, here are some considerations:
1: Look at the encounters, compare them to the XP Thresholds for encounter difficulty in the DMG. If the single dungeon (in this case, the hatchery) contains a few Easy encounters, then the party can handle it in one day, no problem.
2: Consider what makes sense. The party is raiding a hatchery that is heavily guarded. If they roll through, clear half the hatchery, then pitch a tent in a random back room...they are going to either get ambushed, or the hatchery may be evacuated while they are sitting there wasting the day. Or, at the very least, the hatchery will be on high alert and ready for them when they elect to continue...meaning ambushes, traps, fortifications, etc.
So, here are some possibilities.
First, the module may be intentionally straining your players. This happens sometimes. Forcing players to push through when they are short on resources can sometimes lead to some very creative solutions. Alternately, your players might just be burning through resources faster than they should....you really shouldn't be wasting spell slots when a pair of kobolds attacks you. If your players find themselves running short on resources, but still running into encounters, they are likely to become more conservative with their power.
Second, if necessary, allow your players to waste the rest of the day so they can take a long rest. But...consider the ramifications of them doing so. At the very least, they will put the place they are attacking on high-alert. Surprising enemies will become impossible, and I would expect the enemies to dig in and fortify their positions. They might set up ambushes ahead of the players. Or, they might decide that this location is a lost cause, and sneak out. Whatever the case may be, make sure your players know that taking a nap in the middle of an assault is probably not the best plan ever.
So, to give the general gist of it...
Yes, players can always choose to waste the rest of the day so that they can take a long rest. But you have to consider how the NPCs will respond to having a full day to discover what has been happening in their lair.
Best Answer
Mentioned in Chapter 8: Adventuring, the main rule to travel states that a fast speed is 400 feet per minute, a normal speed is 300 feet per minute, and a slow speed is 200 feet per minute. The default, therefore, should be 300 feet per minute, particularly when there's nothing interesting (featureless corridors, etc), and 200 feet per minute when there's any particular need to be cautious (e.g. stealthy), or if they're actually looking for something.
A more detailed blog post (does not quote official material, but looks legit) suggests 5 minutes for each trap/lock if proficient and equipped, 10 minutes otherwise, up to 20 minutes for secret doors/passageways (with an Investigation (Intelligence) check to reduce time), and a general guideline of not more than 10 minutes per room for activities, unless the players choose to exhaustively search a room (20 minutes). I can't seem to find rules for these actions right now, but I remember using similar guidelines in many groups both as players and as DM.
You might want to keep track of seemingly mundane details to help calculate time. Did they spend 30 minutes deciding if they wanted mutton or pork? Did they decide to spend an hour reading books in a library? Not every room is going to go at full speed, and you might even automatically add in some time-wasters to help pad out the time if your players don't do much on their own. Add a lot of locked doors, and traps, and secret passageways, and treasure boxes. These all take time, and if designed well, will take more in-game time than real time.
The rules are a decent start to tell how much time has passed, but you should be prepared to arbitrate various random activities that do consume a lot of time but are not covered by the rules. I had one DM that even advanced time if we took too long deciding what to do in a room, as if our own indecisiveness was reflected in our characters. Be creative, and you can easily find places to realistically add many wasted hours in a day to help your players reach legitimate Long Rest points (preferably near the end of a game session).