Can I use 6" hook and loop disks with a 5" sander?
The holes on the discs may not line up with the ones in the base--if they don't, you'll have to be careful. As you say it will interfere with air flow, which will affect cooling, sanding, and sawdust removal. I'm not sure whether it's enough to damage the tool, unless maybe if you're sanding for hours, but the results may not be as good..

If you do use them, I would recommend cutting off the excess edge--it can dig into your piece and leave marks.