The Nexus 6 is a confounding beast. This big phone doesn't have tap to wake functionality, but it does have ambient screen mode. This way of displaying notifications as they come in might be the reason there's no LED notification functionality built in. There is, however, a physical LED.
The LED is positioned behind the top speaker/earpiece and can produce red, blue, and green light. It's a lot like the green charging LED on the Moto X, but it appears apps like Lightflow can use it for notifications as long as you're willing to root. It doesn't even have to be plugged in, which is what kept the Moto X LED from being very useful.
I wouldn't expect Google to ever open up access to this LED, so if you absolutely must have LED notifications, it's time to root.