Staples cut/break the grain. This will not fix... Wetting it in any way will make it darker than the surrounding wood. Edge grain soaks up moisture like a straw.. You either have to leave for charactor ( Birth-Marks.. as it were..)as others have stated, or try to mix a filler to match.. this usually turns into more of a chore than it's worth. Every spot is/will be, innevitably, in different colored areas and therefore would involved altering color for each hole to make them all right.
I would rather leave and fill with epoxy or use a contrasting color and make them more visible. Showing things off tends to look better than trying to hide them...

If you are serious about hiding the spots, the best way to go about it would be to take a scrap piece of wood and cut little pieces of wood off ( to match colors ) and with a tiny spot of glue, put them in place. This also is a very tedious operation and possibly not worth the effort..

Best case scenerio... Go Stapless...!!! Everyones doing it. But then.. that would mean building another boat..

Rehd
Chillin' @ 51* in
Fresno, Calif.