Not an uncommon issue at all, you're right that he's sleeping in the tubes because he feels safe there and you're also right that it's not very good for him. The simple solution is just to take the tubes away, either permanently or until he gets himself properly settled in a proper nest! The hamster heaven should come with tube blockers or end caps?
You can get him into an earlier routine but it's best to do it gradually so it might take a while, if he's usually up at midnight feed him at 11.45, then maybe 11.30 and make sure he's getting things he WANTS to get up for like fresh veg, a bit of pasta, a tiny bit of cheese etc. Though he should also be weaned slowly onto regular fresh foods if you haven't done that already as giving them too much suddenly can upset their stomachs. He's having some very typical young hammy problems, nothing to worry about you'll just need to be a bit patient