I can't see much effect on aviation - waivers ad grants will be issued to cover any gaps and things will run on as they are. APD is a minor thing to sort out with little operational consequence.
Sadly , the whole thing strikes me as petty, egotistical nationalism. Scotland has more national identity than any other member of the UK and plenty of political independence. They want to be in the EU, but that makes for more regulation and impact on Scottish domestic issues than the UK that they are so keen to escape. And while so keen to leave the UK, they want to retain the UK currency. The only reason for that is that the Scottish economy cannot sustain itself, and by retaining Stirling, they know the UK will bail them out to keep Stirling going, just like the EU bailouts of the crashing Euro users. The nationalists overlook how much money is pumped into Scotland by the rest of the UK through public spending on infrastructure, public sector jobs, benefits (including NHS spending, which is higher per capita than the rest of the UK) and scams like the Barnet Formula.
Scotland have the right to self determination, and I support that, but only a fool would go independent. If they do, then they should not be able to retain UK currency - why should the rest of the UK have to underwrite an independent nation, and if the Scots are so sure about their financial viability, why would they want it?
The no campaign is absolutely right - we're all better off together. No system is perfect, and Westminster does have corruption issues, but less than Edinburgh. And may I remind you that Blair and Brown, the most inept and corrupt PMs we ever had, were both Scots?