Because of the nature of land in Florida, the "underground" Utilidors are actually the ground floor of the building. Then they dumped the sand from digging Seven Seas Lagoon all over the top of it and built most of the Magic Kingdom on that. As you walk from Fantasyland to Liberty Square, past the old Skyway building, the path goes abruptly downhill: this is at one limit of that buried ground floor.
Another limit of that ground floor is one wall of the 20,000 Leagues lagoon.
You can kind of think of the Utilidor wall as a book, at this point. There are pressures from the lagoon holding things one direction, pressures from everything that's been built atop that ground floor pushing the other way. Pull away of those pressures, and like removing a book-end, you risk the whole thing falling the other way.
I don't think anyone is _positive_ that's what will happen if they drain the lagoon, but I think there have been enough smaller cave-ins that the experts think it's a real possibility.
Of course, if you throw enough money at it, even if the problem was the worst case scenario, something could be done. I think the fact that such prime real estate has lain so relatively unused for so long gives a hint at just how expensive fixing 20,000 Leagues is going to be.
It's unlikely the old subs from either location will ever be used as a ride, again. Too much maintenance, too little capacity, too slow to load.