Boolean is a tool, and like any other tool, it's no more inherently good or bad than the way it's used. If you want to use it to, say, put a cylindrical hole through an Orion mesh, it's really good at that, so long as you clean up you're geometry afterwards. It gets its bad reputation because people forget to clean up their geometry, and end up with convex polies and zero width faces and things like that, that make FS2 go nuts.
I find the best thing to do with Boolean is to use it to generate verts in the correct places, and then manually connect the new vets to the old ones in a sensible, efficient manner.