It seems that no one can point out even reasonable issues with the new holy of holies. Any attempt to do so will be met with a star ship load of examples of past ludicrous complaints presumably trying to imply they are all on the same level.
It is not unreasonable to question if a star ship can exist underwater. The pressures involved are enormous and there is no reason any form of flying object should normally be designed to cope with them.
Now maybe there is a way for the Enterprise to operate in water but I have no problem with anyone who is not prepared to sacrifice their reason on the alter of the modern obsession with "Cindy Lauper Trek": Fans just want to have fun (AT ANY COST). So can we avoid this silly self-indulgent ridicule (or at least restrict it to things you are sure deserve it)? Such rampant anti-intellectualism really isn't a good look.
I think it's just a matter of seeing Star Trek for what it really is, i.e. fun, occasionally smart space opera, instead of believing the self-perpetuating myths which see it as first-class cerebral science-fiction.
If your suspension of disbelief can't stand the thought of the Enterprise going underwater, it means that the whole of Star Trek has to be rewritten in order to accommodate the kind of critical thinking you're advocating. In the end, I think that would be futile and won't make Star Trek any better.