PVC conduit crossing a wire run
To answer your main question, having the wiring cross is not in itself a problem.  However it sounds like you may just have romex / NM strapped to the underside of the ceiling, that isn't likely up to code.  In a workshop, I might err towards caution and pipe it all up.  This is not as much trouble or expense as you might think in a single open room.  In a workshop I can picture a long piece of material getting away from you and hitting the ceiling, much better to have the wiring protected if that happens.