No, I mean:
"Flooded" doesn't mean "everything is always underwater".
Having a surface isn't a problem -- their planetary home ocean had a surface -- and lots of equipment can function above that surface.
Fair, I'm been assuming that flooded means
flooded:
I am assuming that aquatics are waterbreathing, though. A lot of this wouldn't apply if they were e.g. dolphins or otters who had to live in water but didn't necessarily have to breathe it.
If they're all surface dwellers and everything will be shallow pools anyway, then 90% of the problems go away; you don't even need to deal with pressure issues due to scale; you just have separate pools connected only by air. And you no longer have to worry about engineering machines to work at everything from 1 atm to 1000 atm (which matters even if you enclose them in a very high pressure air pocket, as even the air behaves differently).
Most of that just goes away if you can treat it all as being basically 1 atm at surface level throughout.
As someone mentioned above, all the problems with water-based environments in space would have already been solved for their space ships, which usually precede Habitats by a good span of time.
It's a massive difference in scale, though.
And spaceship crews (I assume) can have very different requirements from civilians doing civilian jobs, raising children, living normal lives (unless all ships are Enterprise-like).
Ex. Humans have submarines, and submariners stay at sea for months, but that
does not mean that we can just build a city at 5000ft below the ocean.
What carefully trained and carefully psychologically profiled professionals are able to tolerate for months/years at a time and what
every citizen (including children, elderly, unstable, criminals, etc.) can tolerate
permanently are totally different. You can cut quite a few corners and e.g. train everyone to wear special breathing apparatus outside of sleeping/eating quarters, when everyone is a professional. But in a permanent settlement, everything has to be safe enough that a small child can't injure themselves (or break something).
Dunno about "hardest" but it is true that Habitats are implied to have a much larger volume than space ships.
So it might not be the "hardest" problem but it could be a new problem which hadn't needed solving yet.
Sure, it's definitely a problem that needs to be solved. I'm just objecting to the "Everyone who can physically transport enough water (which is every empire) should be able to flood a habitat. That mean needing Hydrocentric is ridiculous and breaks my immersion!" type arguments.
It's believable that it's within the engineering capabilities of every Aquatic empire. But it's also believable that it's
not (and taking Hydrocentric represents taking that extra step to actually smooth out all those engineering wrinkles). There's way more than enough wiggle room that it shouldn't break verisimilitude, whichever way the devs decided to go.