Rob is probably right, however if you want to try a little science:

Mix up some epoxy, add small amount of colloidal silica (a teaspoon per 4 ounces or less), mix it throughly and let it sit for a few minutes. The silica will change the surface tension of the epoxy, helping it level out a bit, as will letting the epoxy sit for a bit. There isn't enough silica to effect the clarity and the sitting will help let air out and improve the clarity

While the epoxy is thickening a bit, take a heat gun and throughly heat the area where your pinholes are so the surface is hot to the touch.

While the surface is still hot, apply a thick layer of your epoxy over the spot and then squeegee it into the holes. Add more resin as needed. The heat of the wood will lower the viscosity, the dropping temps will help suck resin in, and if you are lucky the cavity below is not too deep and gets filled.

It probably won't work, but it won't take long to try, is easier than sanding away and if you are lucky the problem is reduced.