The need for air travel between Scotland and the rest of the UK will remain, possibly increase, also an abolition of APD by the new country would add to this particularly for airlines such as Flybe, Ryanair would likely benefit because APD is a larger proportion of their ticket prices.
Any new country will want to show to the world its new found independent status, so no doubt inter governmental flights would increase across Europe.
idea's of setting up a sovereign wealth fund such as here in Norway is very optimistic, all the papers i have read suggest Scotland will need every last cent in revenue, i guess it won't be pence any more? and then some to cover their proposed tax cuts and spending plans.
The question of borders is interesting, certainly flights between the rest of the UK and Scotland will no longer be domestic flights, in fact Scotland will only have a handful of these, mainly to the Islands & Highlands, are there any flights between the central belt and Aberdeen?
Land borders will also be interesting especially if they hike the price of booze to boost tax revenue and cut chronic alcoholism in the west central belt and this results in booze buying trips south of the new border.
Aviation wise Newcastle could see some flight demand going over the border, but i think its unlikely someone would drive for 3- 4 hours from Manchester to save €15 on a flight?
I think the vote will be very close and it must be interesting to be in at the birth or re birth of a new nation, good luck either way.