I've used Nikwax on my Goretex, plus I have a Barbour. Unfortunately I haven't needed to re-wax the Barbour yet (will do soon) so I can't really tell what it's like. However, at a guess I would say that the Nikwax will be miles easier - just bung the jacket in the washing machine and job's a good 'un. Waxing something from scratch will probably be lots harder than just giving something a reproof.
No idea about durability of the waterproofness, although presumably adding a layer of wax would strengthen the cotton more than a thin film of Nikwax.
Mark