Is there any reason against using red onion, or a mixture of red and yellow onions to make an onion soup?
I would simply use whatever onions I had available! Red onions have a milder flavour than yellow onions (therefore red is usually preferred in salads) and obviously different colour but the difference is still small enough to interchange with no problem. Unless, of course, you desire a particular colour in the soup or are particular about the soup having a strong or mild flavour. Leek would make it even milder and sweeter. If I'd have to make a choice I would use yellow onions and spare the red ones for raw/decorative use.