.RJ this is Brandon from HT.
When my wheels were powder coated, the guy doing the job wouldn't touch them until the bearings, spacers and all relative parts were removed from the hubs. I'm not sure if this was a personal preference or not. I think it had to do with the possibility of expanding parts leading to possible damage to the hub or something else. He also didn't want to risk getting any melting greese or rubber on the powder as it was being baked.
DO NOT have the inner hubs powder coated as this will throw the specifications off and you may have a really really hard time pressing in the new bearings and what not. Powder coat will also jam up any threaded areas such as the locking spacers that go on after the dust covers. I included this picture of my rear wheel as a reference. The powder coater will use a special heat resistant tape to cover any part that should not be powder coated. What color are you going with?