Hamster not leaving nest

[souffle]

I'd advise you to remove the penthouse and tubes and use the blockers to close off the holes. You should have had them with the cage. The pod isn't healthy and they can get chest infections and food goes bad in there. If he's a good size then he might get stuck in the tubes! Put the deep bedding under the shelf and let him nest there and leave some space free for the wheel and the other toys.
Young syrians don't drink that much and if you are feeding some fruit and veg he is likely getting enough from that. They are desert animals and their kidneys produce concentrated urine so don't sorry he will be drinking enough. Check the spout every day that it is free flowing. I'd use a traditional bottle and not the sippy as they can struggle with those to work them.
If he is confident I would start handling. First a lift and lay back down them allowing a hand to hand run through your fingers made in to a tunnel so he feels secure with the hand around him.
It's warm just now so they are quite sleepy so ensure he's in a cool shady area.