Depends.

When I made the stock for my rifle I left as many objects as I could by themselves (not combined) so I could keep the meshes simple and thus easy to modify. When two parts join together in real life, but there was no reason why I should do so in Maya, I made a division in it, moved some verts near the edge and moved the verts on the edge out away from object so when I made it smooth it would simulate soft edge without having to combine and merge them. Sorry if this is a bit incoherent...