Well, I gave it a go, and as far as I'm concerned, it worked a treat, really.
Clearly not as professional-looking a result as you'd get by cutting with scissors then stitching the edges and shock cord hole to stop them fraying, but good enough for me. If you're planning on re-using your homemade nomex protectors and don't want them to fray, but can't be bothered with needlework, this is an option, at least.
As expected, with nomex the hot knife does NOT just effortlessly glide through the material as it does with nylon/polyester. The knife is actually burning & cutting, rather than simply melting the fabric. But the resulting edges do seem to be "sealed" enough that they look like they're going to resist fraying (for a while at least).
The knife needs to be RED hot. I was managing to cut no more than a couple of inches at a time before needing to put the knife back on the flame.
My tips would be:
Use a sharp, broad-bladed knife
Use a plank of wood (that you don't mind trashing with burn/cut marks) as a cutting board.
Get the knife red hot for each cut and press hard, cuz nomex is tough stuff.