Hi,
The epoxy I use (Bote Cote, an Aussie brand that's simply sensational) doesn't darken the wood much. I think others are the same.
The best idea is if the boat is oging to be natural wood, to look at the varnish you'll use. You can get completely clear varnish which will give you a natural, light coloured wood, but also ones designed to be "amber" or "warm" as well as tinted varnishes. The amber ones (I do't think this is the correct term!) give a subtly darker, deeper wood colour without actually tinting.
Check with a marine chandlery and ask what they recommend for a deeper wood colour or tinted varnish.
Hope this helps.
Darren