Electrical – How to qualify for the 75C table in the ampacity chart

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.

The only sure way to hunt down missing wires, without taking forever, without disturbing the walls, ceiling, or floor is to use a circuit tracer. I use a Mastech MS6818. It comes with a transmitter and a tracer and can be used on energized and unenergized circuits. It may be worth a homeowner to have one if he owns a house like yours and you are determined to track everything down. You might find a local contractor who also has and uses such a device, but I wouldn't let him in unless he has one in his hand when he comes to the door.

If all of that is too expensive your only other option is to verify that it is not a switch leg or some such and doesn't go anywhere. Then just wire nut it off and leave it in the box, then at least keep a mental note as to where it is in case you find something not working.

Good luck and stay safe.