"There will also be specific government ICT issues: an independent Scotland may have to build its own communications intelligence and surveillance capacity - GCHQ's three main offices are all in England - and the same may be true for defence ICT. "
This is an interesting one - what do those organisations do if next week they discover that within about ~2 years a certain percentage of their employees, with varying levels of security clearance, are possibly going to be citizens of another state?
Maybe they could go on a fact-finding mission to Moscow and ask the KGB and GRU how they coped?