If the vote goes to a Yes, i think there will be retrenchment of UK airlines from Scotland. At present as EU operators, we can fly EU-EU, and EU-non EU. However if Scotland does go, and as is suspected ceases to be part of the EU, it restricts where EU airlines can fly from EDI etc.
There won't be any issues flying Scotland-EU, but Scotland-non EU will be difficult for EU airlines. There's a lot of charter trade from Scotland to Egypt & Turkey that have to find another option.