First off, reducing the surface count has a HUGE benefit for performance. And each child object is its own surface. Thus, merging everything together into a single object/surface at the cost of additional polygons is a smart tradeoff.
Second, avoid booleans. Booleans are evil! They do all kinds of nasty things to your models, like lots of tiny splinter polygons and cracks in the mesh. Just say no. I'm sure Truespace has some sort of combine/merge function for putting together multiple meshes into a single object WITHOUT doing any sort of boolean operation. I've not tried in Truespace specifically, but every modeling tool I've used has a function like that.
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