Well, I wiped and looks like LED does not work even on pure AOKP - is it only me? 2014-10-23 version here :S
To be detailed - LED works when charging, but once I get a message or an e-mail, it blinks once and then never blinks again for this particular notification. Weird that if I unlock the phone and relock again, it'll start blinking when there's still some notification active.
you can set the LED in Rom Control LED settings. There you can set for every App you want a different setting so eg. the blinking time, clolor and more. For me it works ok with Aqua mail, Stock sms/mms and more.