If you think the bubbles are big enough to flutter in the passing air stream, then repairing the roof makes sense. To repair, get appropriate adhesive for EDPM rubber roof. Slice the bubble in the middle only long enough to insert adhesive, then use a rubber roller to distribute and bond adhesive to both roof and underside of membrane. Use Dicor self leveling caulk to seal the slice and you'll be good.
Edit: Old Scout says it's fiberglass, not EDPM. Ignore my EDPM repair. Fiberglass is a much different material, as OS said, if it's not leaking, leave it alone.
Bob & Donna
'98 Gulf Stream Sun Voyager DP being pushed by a '00 Beetle TDI