A quick thought experiment. Perhaps instead of looking at the species objectively and deciding whether or not they belong in a specific "biome", we could instead (and I think this might be closer to how
@CGSwans envisioned this round - correct me if I'm wrong) focus on how they're exhibited in the zoo. Does the zoo keep the tapirs in a habitat in which the freshwater ecosystem plays an important rule? Does the zoo give the tapirs a lot of space to swim, or even have an underwater viewing area? Does the zoo highlight the aquatic behaviour of tapirs? If the question to any of these questions is yes, then in my opinion there's no doubt that tapirs and their presence in the zoo should "count" for this challenge. On the other hand, if the zoo does nothing to highlight this behaviour and/or barely has any water in the exhibit at all, I think it's obvious that tapirs should not count.
Some examples to illustrate what I mean: Tapirs in the Antwerp Zoo are kept in a "wetlands" area, next to exhibits for hippos, nutrias, pelicans, a large aviary for storks and ibises, and kept together with geese. They also have a nice and deep pool that they frequently use in summer and can completely submerge in, and as a visitor if you're lucky you can stand on a bridge with multiple tapirs in the water on one side, and multiple hippos in the water on the other. I think it's fairly obvious that Antwerp portrays Malayan tapirs as a relatively aquatic species, and in my opinion they should count there.
On the other hand I'll use the Singapore Night Safari as an example - A fairly decent enclosure with a very nice backdrop and an amazing vibe, but with a pond that is off to the side of the enclosure and in a tram ride setting that focuses mainly on species of open grasslands and tropical rainforests. The freshwater aspect is (as far as I remember) not really mentioned extensively on the tram ride, and while I do believe it is a good tapir exhibit it doesn't really scream as if it belongs in a freshwater setting - So I'm less certain Malayan tapirs would count there.
This is all, of course, very subjective and doesn't really work that well when compiling and comparing lists of the two different zoos - But that doesn't have to be a bad thing.