This is a question for the ages, the last time we went to typhoon lagoon, it was all over the map... some of the ride attendant said you can hold the water shoes, some let you ride with them on, the high speed water slides, I do not think that they will allow you to ride holding your shoes, safety being the reason.
The water socks might do the trick... I personally have never used them... I am going to check them out..
As well I think it depends on what type of water shoes you have if they will let you ride...