Can you use the native HomeKit support?

Trying to understand what it buys me to switch to using the HomeKit component of home assistant vs using the native support of HomeKit that comes with let’s say the hue bulbs.

You can use both, HomeKit component will make non working devices work on your phone using Siri.

Can you exclude them from the HomeKit component so they don’t show up twice?

Yes, absolutely! Actually I just use a include.yaml and just place the components I want to show up on my phone!

The HomeKit component allows me to use Siri, or the HomeKit app, to control various devices in my home that are not natively HomeKit compatible.

I’ve had home automation as a hobby since 2006 so most devices in my home are based on home automation technologies predating both HomeKit and Home Assistant! Nevertheless, they are all now controllable via Siri. I can tell Siri to lock a door, open my garage door, dim a light, increase the temperature, arm our alarm system, etc.

Here’s what I have in my configuration.yaml file. I only include the devices that my wife and I feel are convenient to control via Siri.

homekit:
  auto_start: false
  filter:
    include_entities:
      - light.kitchen
      - light.sink
      - light.mantle
      - light.foyer
      - light.hallway
      - light.tablelamp
      - climate.thermostat
      - cover.garage_door_opener
      - lock.laundry_door_lock
      - alarm_control_panel.security_system
  entity_config:
    alarm_control_panel.security_system:
      code: !secret alarm_panel_code

Frankly, it took me less time to get the HomeKit component operational than setting up all accessories within the HomeKit app. However, after you’ve configured each accessory to reside in its appropriate room and included it in groups (we use Upstairs, Downstairs, and Outside) you can issue commands like:
“Hey Siri! Are there any lights on Downstairs?”
“Hey Siri! Dim the Family Room lights.”
“Hey Siri! Set the temperature to 22 degrees.” (Celsius)
etc