Should I do a second sanding with finer paper (120 grit) or would this be a waste of time best.

Yes I would sand with a finer grit.

When the glass and epoxy are applied, will this difference disappear, remain the same, or be heightened?

Normally everything is accentuated with epoxy.

How much will they show when glassed, and should I sand deeper to try to get rid of them?

Yes, they will show up and probably worse than what it looks like now with only wetting down. I would try scraping with a curved cabinet scraper before sanding. When you sand you also sand the surrounding area of wood, while a cabinet scraper is better at spot cleaning the harder epoxy. Once removed touch up with sandpaper. Only you will know haw far you can go with sanding before you expose secondary layers.