I'm guessing that maybe you've seen Daniel's design over at mag-racks.com? He uses black egg crate now, which is visually low-key - he used to spray paint his black with Krylon Fusion. I think he encapsulates his (uncoated neodymium) magnets in clear casting resin, also using the resin as the adhesive that bonds the magnets to the egg crate. A little research showed that one technique used to encapsulate the magnet is to drill appropriately spaced holes in a plastic cutting board and using duct tape to seal off one side of the hole. This makes "wells" that you can partially fill with the resin/hardener mix before dropping in the magnet and setting up the egg crate for bonding.
I think that your epoxy paint approach would be cheaper for small quantities since casting resin is kind of expensive.
Thanks for the answers. I've been kind of wrestling with, should I build my own magnetic frag racks, whether I should use 1/8" or 1/4" discs.