You aren't limited to having unique DID if the vsans don't touch. Each vsan is completely unique and vsan X, domain Y is completely different than vsan A, domain Y. Imagine that if the sans are physically separated, then domains do not need to be unique. So, when you logically separate them, they are still separate and can have the same domain.

If you think about it from an IP network point of view, the vlan A can have the same IP subnet as vlan B if they never attempt to contact each other or route between them.