I set up Home Assistant recently on a Raspberry Pi, and imported all of my Hue lights. So far so good, but I haven't managed to migrate completely off the Hue app + Bridge. I've purchased an HA-compatible Z-wave dongle, which will apparently let me manage all of my Hue hardware without an account or bridge, but haven't tried taking the plunge yet.
I hope you meant Zigbee dongle instead of Z-Wave. Hue devices use Zigbee and can be directly paired to Home Assistant using a Zigbee dongle, but not using a Z-Wave dongle.