Do the waterparks operate at a loss? Seems odd to me since other water parks successfully operate and make profit, at least enough to stay operating.
Are they profitable? Yes. Are they as profitable as the parks, Disney Springs, resorts, etc - no. Have to look at the whole picture though - things like water parks encourage people to extend their vacation, stray less from property, etc.
Staffing is a BIG reason they are currently closed. Custodial was needed for the parks, any classified as attractions host/hostesses were pulled to attractions in the parks. CPs are a huge part of water park staffing, etc. Opening them for the summer was considered early on, but it would have been more trouble than its worth to make happen.