If it's a boat ride, the ride will be on the bottom. That's a lot of water weight to have to support on a second story unnecessarily. Putting it on the bottom also allows for parts of the ride to have more height for big scenes. It's not that hard to get guests to the second story. Elevation changes outside gets some, then just built in ramps themed as village paths inside.
I wondered about the water weight issue myself. But I did poke around and saw examples of water attractions on upper levels. Beyond the classic flumes all over the world on steel supports, I found that Pirates of the Caribbean at Disneyland has the Blue Bayou on a second floor with a lower level of attraction scenes below it. Splash mountain also has water on an elevated level with scenes below.
Good point about perhaps wanting taller show scenes. Those could come after one or more drops, mid-ride. For example, halfway through the ride if there's a 15 foot drop, there could be a scene that's 55-feet high, if it later drops another 10 feet there could be a scene that's 65-feet high. These areas where the height of the ground level (where I'm suggesting the retail/F&B are) is encroached on from above could be over the backstage areas like kitchens and stockrooms where the height can be diminished greatly from the 40-foot shell height (the kitchens only need to be, say, 15-feet high anyway, for example).
By the way, I know that if the attraction were on the upper level it could result in a lot of support columns in the retail/F&B area below, but I think that could be a blessing as much as a curse. An inspiration for the vibe of that area could be the International Market in Waikiki, which is this shopping area in a forest of tropical trees. I was there about 30 years ago and sitting in there, having a beer, it was an amazing vibe with all the trees around! Basically all the structural supports for the level above could be thematically
dressed as trees, with a maze of shanties, bridges, and docks between them (I included some images).
