Probably wise to remove them. They can go with the head, if there is room. Just wrap them in some bubble wrap and put them somewhere where they won't get smashed.
I have had good luck just putting something between the top of the tube and the top of the box (to keep it from rattling loose) if your 12ax7s have the metal sleeves, they should be OK. I've done this just shipping it in a cardboard box, When I had flight cases for everything, I would just put it in the flight case, and send it. I never had a problem with anything in a flight case.