On the surface it seems that the shrubs and trees do die in evil biomes at a certain rate. Although, as long as that wasn't one of the last few of trees they'll still reproduce reasonably. Leave thirty trees and kill the rest if you really have to. Leave more if you can to up the spore rate. Conservation is a vital skill of sorts if I'm right........... Evil/haunted/terrifying/sinister means both attacking skeletal/zombie creatures and gradual tree-lessness. That's what's Evil about them.
Underground it's hard to tell. If you don't have the whole cavern mapped, and haven't only set the world gen to have just one cavern, it's impossible to tell. Three caverns entirely mapped is hard.
Absolutely, non-empirically, as well as probably completely wrong, I can tell you this. Even if you think you don't have any trees and your biome can't grow any, you'll always get "tower-caps" in wet/mud soil areas if that was your only wood on embark. Take "tower-cap logs". But that's probably my stupidity on game reasoning.......
And strangely enough, if I'm right about that, then take less "whatever small pest" brains on embark. Give your cat a break. No one needs that many types of FPS reducing "foo" to get a free barrel. But as an aside, always edit your embark to bring fish/turtles/losters......
If you have them in the biome, they MUST exist...........