Shouldn't really cause any problem. I have been through the same process a couple of times recently (actually am in the middle of it again). Obviously tracking peoples whereabouts and what you have been up to is important, but I understand your concern about having an 'empty' period in your employment history. I have had many such periods recently, but all you require is for a personal referee to confirm where you were during any gap periods. This does not affect the disclosure scotland process (as this is purely done using personal details such as name, address etc), but will be something your next employer will need confirmation of to provide the airside pass issuing authority with. Simply, as long as you know someone, who will incidentally have had to have known you for 5 years+, they will be able to provide written confirmation to backup your application.
The only thing you should be aware of is that it is a time consuming process, and many potential employers will expect you to have most if not all the reference information available on application for the job, to prevent unnecessary delays. So basically it is in your interest to think where you have been the last 5 years and have referees prepared to cover said period.
Good luck
FD