Thanks, but since I was root, the permission issue wasn't it.
Turns out there's some notion of RGB lock in the LED driver for the Nexus 5. To make the LED's do things you have to bracket your changes with writing 0 to rgb_start, then make changes, then when you write 1 to rgb_start you'll see them. I now have a nice blinking red LED, which will be quite handy for visual indication of new notification!
(Asiek777, thanks for verifying that it wasn't a hardware problem on my end.)