If Scotland leaves the United Kingdom what will happen to the jobs of Scots in the army, navy and airforce?

Scotland would be finished. All the weapons that Scottish Regiments use, belong to the Ministry of Defence, not Scotland. All the Navy ships and planes belong to the Ministry of Defence, not Scotland.

They would probably be the basis for a Scottish Military.  

they will either disband the Military in Scotland or Build a Tiny defence force because Scotland will be a 3 world country within 10 years

I imagine a deal would have to be worked out , to either grant them some special status to stay on........or change the law to allow  "foreign nationals"  to join. 

Or they could simply stop accepting them, and slowly phase them all out. 

Not much, unless bases in Scotland are closed

Gone, they would have to resort to haggis farming.