Retro Studios didn't do any water levels for this game because they found is slow, but if you really think about it, there is actually some logic behind it. The Tiki-Taks? They're made of wood, and some of them are on fire. What would happen to either once submerged?
Even better, Tropical Freeze features as the enemy a bunch of penguins, walruses, polar bears and other arctic animals in a Viking horde. Those guys are associated with water, so it makes sense that Under the Sea and other swimming levels would return in that game.
All the tunes that return from the first Donkey Kong Country have "Returns" slapped on the end (e.g. "Life in the Mines Returns"). The sole exception is the "Jungle Hijinx" theme. That's because the theme has been used in pretty much every Donkey Kong game in the interim, and never really "left" in the first place.