I don't see why the UK would keep their nuclear arsenal in Scotland. Especially since nationalists have tried to get rid of trident for quite a while now. I think it's one of the positives for the 'Yes' campaign. And this will probably be done within a decade or two.
Aside from that, on the whole defence spending front, I do think Scotland stands to lose long term. When it comes to defence spending, the UK will take into its fold a lot of contracts sourced to Scotland purely as a security measure. That's why some in Scottish defence industry have been a bit upset. They'd still be able to get the international contracts though. Or at least bid for them.
And they will lower their own defence budget of course - there are significant savings to be had there. So overall, bad for the economy good for the budget.
edit: I should add that the last line is for Scotland. The UK loses substantially more than Scotland in my view.
International contracts would be tricky for iScotland's defence industry, but not impossible. You'd need a long term stream of orders to prevent decay, and there's a lack of nations looking to buy frigates right now. There's also the problem of putting together a decent package for orders. The rUK, US or even France can tie an order together with advanced training for the ships and systems being sold, as well as broader defence agreements. That's not something iScotland can really offer at the moment.