My new Nanocom arrived today which I'm going to use on a number of vehicles.

Plugging it into the RRS today it came up with 59 - FIFTY NINE faults, some historic and some intermittent but only one permanent (FBH lockout) Is the best action to clear everything and see what comes up over the next few days or should I investigate each one?

Yes; clear them, and see what comes back after a drive cycle.

Edit: Oh, and best to fill in your vehicle profile too (if you think you have already, it's normally the colour people miss out ).  Visiting from DISCO3.CO.UK
2006 Discovery 3 TDV6 Auto HSE Zambezi Silver