It's true they haven't been upgraded in many years, but I don't generally go to a water park and expect thrill rides. The original Schlitterbahn in New Braunfels, Texas hasn't been upgraded in nearly as long, and they are still really busy.
It just may be a case of all the locals checking out the new guy, as I'm sure will be the case with the new
Epic Universe as well. While everyone appreciates new tech, and better themes, not everyone wants roller coasters. There's still a place for for well themed flat rides, trackless rides, and omnimovers.
I don't think I'd classify them as "in trouble" as water parks are pretty cheap to operate once they are paid off, and Disney's should have been paid off long ago. It is just the liability/injury insurance and CM/labor that are major costs, and that is certainly controllable for Disney by having only one water park open at a time.
It could also be that water parks, in general, are not the draw they used to be, except for some locals, as every resort on site has a decent pool, and people are shortening their trips due to cost, that would even be true of Universal.