As @cstory777 pointed out when the skill was originally released, the new Alexa Skill does (or did) specifically hide Hue devices. They're still shown in the device list in Habitat, and you can check or uncheck them, but they're silently ignored when presenting the device list to Alexa. As the skill says,
If you include a device that isn't compatible with Alexa it will just be ignored and not sent to Alexa.
As far as I can tell, having once again checked some Hue devices and asked Alexa to discover devices, this still seems to be the case.
