more of a problem, with the the lowpoly than the high, though you will get a better edges, if you model it in, or float it. and even in the lowpoly you can get by complications with projection by simpley explodeing the mesh, and bakeing that way.
Intersections can create aliasing if the baking tool doesn't multisample when it renders the projection to create the normal map. But usually intersections are the worst on the lowpoly model, because they complicate the projection.
In the lowpoly more-so than the high. I try to merge as much as possible in the low, and only have separate mesh chunks for areas that need to animate or complex overlaps(in which case you need to explode-bake them). In the high, generally the more meshes the easier it is to work with, obviously if you're modeling…