: while I was doing 150 grit sanding, I noticed some small pits in the epoxy.
: pin head size. Will the several coats of varnish fill these in?

Pin Head sized, i.e. ~ 1/16"? Well, you should probably fill those with some clear epoxy first. Best to get defects taken care of before you start varnishing.

Varnish will fill eventually, but it takes a lot of coats and sometimes a hard sanding around coat #5. Horizontal surfaces fill quicker as the varnish tends to puddle in the low spots. Keep in mind, as well, that gloss of the varnish will tend to hide minor defects like this.

Craig