I don't see anything wrong with him going to hide. Both Zoee and Taz just leave the room while I am vacuuming.
But if you want him to get used to it, maybe you could try the same thing you did when hubby started the bike. Have Chopper on leash standing next to you. Have someone start the vacuum and just stand there. It may be past this point now, but it's just a thought.

When he goes and hides does it take a long time for him to come out? And is he shaking? If no to both of these, maybe just don't worry about it.