Hello,
I'm wondering if anyone can recommend a cutting bit (preferably with a 1/4" shank) that mills nomex honeycomb nicely.
Thanks!

Most of the cutters that work well for honeycomb have a combination of a heavy teeth in the body of the tool and a round knife at the bottom - so they cut the surface clear and then shred the rest.  They're nice and expensive.  For some cutting the tool is held at a small angle to the surface that is bring cut so a 5-axis is necessary. Here's a small one with a .25" shank:  https://corehog.com/product/small-size-finishing-tools/#small_corehogger

It can be messy and hold-down is an issue if it is not already bonded to a skin. You may find that a carbide burr (like this: https://www.mcmaster.com/8785A24/ ) or a chip-breaking rougher works ok but it may tear stuff up.  Surfaces can be cleaned up using an orbital sander an 400+ grid paper.  It removes the fuzz and leaves clean sharp edges for bonding.