Hello @haussmannj_ ,
Best way to do it without disruption of service would be to ND-ISSU [Non-disruptive upgrade].
You need to check the upgrade path from 6.0(2)A8(9) to 9.3(8), you'll probably not be able to jump to 9.3(8) directly from 6.0(2)A8(9).
Regarding the question: Can both switches run on different VPC version?
--> No, it's not recommended. It could work but it could cause as well a lot of inconsistency. Best is to upgrade one VPC leg, then the other.
Hope it answer your request.
Kind Regards,
Antoine