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.

https://www.neuhaeuser-controx.de/services/composite-tools/honeycomb
Very expensive, really necessary 5-axis HS spindle included. I tested 4 flutes carbid router on 3-axis machine, it really doesn´t work. No cutting rather pushing...
The carbide burrs Chris talking about are for cured panel machining, not for honeycomb cores.
If the core shape is quite complicated I don´t know another method how to machine it.  If the core is flat, resp. constant thickness all around the area and you would like only an edge bevel all around, for example chamfer 3x45°, I use angle grinder with sanding wheel P120. Bond it using spray glue on MDF pattern and sand it manually. If I have a complicated core that´s the reason for Rohacell using instead the honeycomb. There is no problem with 3D machining or thermoforming.

I forgot to mention that density of the honeycomb matters a lot.  Heavier material will be more stable and easier to machine but under 40kg and it will be a mess unless you have the right tooling.  

The burrs will - in my limited experience - work but it will be nowhere near as nice as the special cutters in the links we both posted - Neuhaeuser and Corehog.  You have to go faster than you think feed-wise and it will tear up light honeycomb.  The burrs work ok because they are almost abrasive instead of trying to take chips like a fluted cutter.  This is way easier if the honeycomb is already bonded to a bottom skin... but doublestick tape, temporary glue and maybe this product:

https://www.airtechintl.com/blog/new-corehold-p-ha

or something like it will help.

But yes, Rohacell is very nice for this kind of thing!

Thanks for the responses, all very helpful!