I always clear the same areas of plants that I do wood, if for no other reason to have more things to brew into alcohol. The above ground farming especially helps during sieges when your hunters aren't able to go out (or worse get stuck out there and killed). It also gives your weavers more variety in plant threads.

I'm one that normally makes a castle style keep above ground with an 'airlock' drawbridge system for the trade depot and plenty of fortifications on towers and walls for crossbowmen to kill whatever happens to be mad at me.

My current fortress is like this and I am hollowing out the nearby mountain from underneath since it is rich in magnetite and native platinum.