You seem to have a very tidy mind, Rov - most people aren't fussed by this.
If your loft is a habitable space, I can understand why you might want to make it look tidier and it depends how much effort you want to put into doing it. Some people are happy to have it just neatly held down using cable clips - these nail into the joists.
Drilling holes in joists in covered by 'rules' in the form of Building Regulations - these are structural components. That much said, small holes for electrrical cables drilled in the middle of a joist are OK and within the 'rules'.
If you are going to do it, do one section at a time - working out what is live using a meter and cutting the dead cables. Then work out where each section needs to be re-routed to - and do it one section at a time. Means running back and forth to the main switch on the CU, I'm afraid, but that is safest and less liable to go wrong.