First of all, if you don't know already, a hint brush has only one surface covered with the hint texture. To construct a hint brush, construct the brush with the SKIP texture and then apply the HINT texture to just one surface of the brush.
Yes, it's okay if the hint surface intersects with a world brush, or even another hint surface. Normally, though, if you're applying it correctly, it would intersect with just an edge and not actually cross the surface. An exception would be a doorway with an irregular shape.
For instance, if, by "irregular shaped," you mean an arched doorway and you want a visleaf to be created at the doorway, use a single vertical hint brush and have it overlap the entire arch and the rest of the doorway, one brush covering the entire opening.