Yes! You can absolutely visit a water park in the morning, then DisneyQuest later in the day.
It will not require the park hopper option on your Magic Your Way ticket because your theme park tickets are different from the added water park admissions.
On our last vacation to WDW, we spent two days in which our mornings/afternoons were spent at a water park and our evenings were at DisneyQuest. Here's some info to help you figure out how to best utilize your tickets:
The
Water Park Fun and More option that can be added to Magic Your Way tickets provides you with separate admissions to Blizzard Beach, Typhoon Lagoon, DisneyQuest, ESPN Wide World of Sports and a round of golf at Oak Trail.
The number of visits you receive with this add-on is based on the amount of days on your Magic Your Way ticket.
If you have a six day ticket and add the Water Park Fun and More option, you'll receive six visits to any of the above locations.
If you go to a water park and DisneyQuest in a single day, it'll require 2 admissions/visits. If you go to Typhoon Lagoon in the morning, depart and then return to Typhoon Lagoon later in the day, it only counts as one admission.
A good way to remember what constitutes a "visit" is that if you are entering a turnstile for the first time that day, you've just used a visit. If you are returning to the same turnstile in a single day, you are still using your same-day admission.