Either thickened epoxy or Famowood wood filler...

There is no need to fill the holes, as they will fill automagically during the building process. Most of the filling happens when you fillet the seams. Any remaining void gets filled when you glass the exterior. And even if they did not fill, it would not affect the integrity of your boat in any way. -Wes

Some people have experimented with filling stitch holes for aesthetic reasons, but most have found it's hard to get an exact color match by the time they're done with the epoxy process (different woods and fillers change color differently when coated with epoxy resin). 

There will be a few drips that run through the larger stitch holes that are not in an area with wide fillets, but you can either scrape them off while the epoxy is not fully cured (gets much harder after a few days) or if you're really concerned, you can cover the stitch holes with blue tape on the opposite side of the wood that you're applying the resin to.  Just make sure to remove the tape within a few hours or you run the risk of it bonding with fully cured epoxy and being even more of a mess to sand off (tape is not supposed to bond with epoxy, but I've found that sometimes at least part of the tape does stick if you leave it to fully cure). 

Or, like most builders, just ignore the holes and sand or scrape off the few drips.  They willl fill in with either fillet or resin during the process. 

On the Wherry, the vast majority of the stitch holes do not get covered with glass or fillets, so they seem prone to being a nidus for drips.

I'm leaning towards trying the Famowood wood filler.  They have a water based formula, so issues with epoxy bonding should be mute (I hope).

Thanks for the input folks.

Hickory

regular Famowood w/acetone base works just fine under epoxy, at least under WEST resin. Been using Famowood & WEST for a few decades and never had a problem. But as many mentioned, epoxy coats will take care of the stitch hole problem. Drips, runs, and sags are easwy to dress offf with a scraper - I use a sharpened with a mill file Red Devil or my cabinet scrapers while the epoxy is green - easy breezy.