Problem is Courtney that "basing UK military assets in Scotland with a possibility of independence," isn't a military question - it's a 99% political one. The simple fact that the SNP wants no nukes in Scotland is typical of the political issues - and the decisions will all be made by politicians, not the military.
An interesting questio is WHO would command the Scottish military - I haven't seen many SO's (or even ex-SO's) who have volunteered to help out..............