My family will be going in about 3 weeks. Most touring guides advise avoiding the main parks on extra magic hours days if you don't stay on Disney property (like us). However, I'm curious to know if the water parks are different and should we avoid the day the water park has extra magic hours in the morning or try to hit that park in the afternoon.
I'd advise to just go to the water park as early in the day, no matter which day you go. We have always stayed on Disney property but we have been turned away if we arrive at a water park mid-morning during August. I'd rather get there early, and expect to leave early. We don't bring much with us – just a towel, sunscreen, and T-shirts. We don't bother with food, drink, scouting out chairs, etc. because of the volume of people. I've seen them trample each other when the parks first open diving for that "perfect" chair in a location where they want to park their stuff. I've also seen those same chairs taken by other people when the first group decides they want to swim. It's much easier just to walk around – sit where you can when you want to rest – go on the lazy river rides – just put your towel in a locker or, even better, leave it around your neck – you will dry almost instantly in the hot Florida sun, anyway.
Assuming you have a park hopper pass that includes water park access (and you aren't paying for a single-day admission to the water park) there is no financial impact on just going to the park for awhile.
Look at the day's weather forecast before you make the decision to go to Blizzard Beach or Typhoon Lagoon. Since thunder showers are abundant in the summer, the parks may have to temporarily close due to lightening. You will also see people running for their lives at the sign of rain, as they feel a need to take cover from water that falls from the sky even though they are already wet from pool water.
I have not yet experienced a water park on an extra magic hours morning. I suspect that if it is the only park offering early hours, it will be more crowded than usual. If they also offer a theme park the same day with extra magic hours then I'll bet more people will be at the theme park. That information can be obtained on the Disney website (exactly which parks are opened early and late on the days you will visit.)
Tips – bring your own ponchos, sunscreen, and umbrellas, and wear waterproof shoes and light clothing that will dry in case of rain.