I was thinking some areas of the museum may have even been underground. The fossil exhibits would have made sense for how dark and moody they were, and I noticed in the big shark tank there were portholes at the back, maybe it's underwater? I wouldn't be surprised if you had to go down a flight of stairs to see some of the exhibits!
Every building in every animal crossing game has been this way. The museum always looked small to me and all of the houses are definitely smaller outside than in.