Of course, this only works when she is wearing an outfit you'd normally expect someone to wear panties with, such as a school uniform.
While there is ambiguity as to whether or not Aqua is wearing the bottom piece under the skirt piece, she's still wearing (at least two thirds of) a swimsuit. It's not an outfit you'd normally expect someone to wear some sort of underwear with, and thus not a candidate for the pool.
Besides, she is wearing the bottom piece. You just can't see it because she uses her goddess magic to make it invisible wwwww