There's not a lot of guidance there for the DM. Here's the text:
"If the eggs are left here, they hatch in less than a week. If they are taken away, whether they hatch depends on how they are stored and treated. Away from a warm, humid environment suhc as this chamber, their progress halts until they are again in a suitable incubator. The dragons can be killed easily if the eggs are smashed."
Everything else is left up to the DM and the players.
What is particularly interesting about this is that, apart from being open-ended (and I know a lot of DMs will not want the complication of the eggs), the fate of the hatchery is something that is addressed in the Rise of Tiamat, with several NPCs giving differing opinions as to *what* should have happened (and possibly criticising the players for their choices). I wish I'd had Rise of Tiamat when I was running this, just because it would have alerted me to many more ideas as to what could happen.
Is this a flaw in the adventure? Honestly, I don't think so. A large part of it could comes down to a disconnect between the writing style of the adventure (which tends to trust the DM to adapt according to the actions of their players) and DMs who are used to a lot more of the detail being spelt out.
Cheers!