Booleans always leave messy meshes behind. I think it is because of the different resolutions of the parts that are being booleaned. Like the circular holes in you example; they have many more vertices around the edge than the cylindrical object they are booleaned through. The verts have to be connected, or the mesh will broken and/or be ruined by smoothing; so additional triangles are made.
Bryce seems to only export meshes (triangles) and not polygons (quads). I always have terrains and rocks and everything come out as all triangles, never quads. I can untriangulate most of them with Wings3D, so it isn't that big of a deal, but Wings won't fix all of the triangulation caused by the boolean process. There are just too many verts along the some of the edges.

Friends don't let friends use booleans.