If you want to fill the little holes up you can simply mix a little epoxy and fill it up, let it dry, then re-sand and polish, voila it looks like part of the wood! (well, a black spot in the wood, but at least not a hole anymore) That is of course, assuming you don't like the more natural look of letting the pits show.
It's all a matter of personal taste. Some handles look good with pits, others not so much, but ultimately the beauty is in the eye of the knife-holder.
FWIW I think this handle looks good either way, pits or not. The only time I say that filling up pits is really necessary is when they are bordering one of the bolts.
Please don't take any of this as criticism, just more or less trying to elaborate a bit for other readers too. You did a great job for your first rehandle and a great job period.
How did you finish this handle if you don't mind me asking?
Personally to finish handles I'll sand anywhere from 400 grit to 1,000 grit, then buff on an 8 inch buffing wheel with white and pink rouge. That tends to get them shiny as can be and fairly easy to maintain with oil. Most stabilized woods take to polish very well, I truly enjoy working with the stuff.