Yes he's upset you took the tubes out but you did the right thing. My suggestion would be to give him a new house - he'll then be happier than when he had the tubes and build a big cosy nest in it. They do get very upset when they're nest is messed with.
They need a house/nesting box that is dark inside and big enough to build a large cosy nest for winter. Putting a bendy bridge tunnel over the door helps make it dark inside. You could buy one or make one out of a shoebox. With a hamster heaven it could sit well under one of the shelves or, as some people do, remove one of the shelves and keep the solid shelf - a flat roofed house can then make another shelf or level.
For a shoebox house - cut the base out of the shoebox, keep the lid as a lift off roof and cut a hole for a door in one of the long sides near the end (that means the other end of the house is dark). They do best with a house that is open underneath and sat on top of the substrate so they can have normal behaviours like burying hoards under their nest or burrowing down. The flat roof also makes an additional level and a bendy bridge over the door makes a tunnel entrance and makes the house darker inside, plus provides a ramp to the roof. It is also big enough to fit a corner litter tray inside (if they have a large house they often move their toilet area into a corner of the house. They usually build a nest at the end furthest away from the door so putting the litter tray at the door end works best (back corner).
A house with a lift off roof is good because then you can check inside without having to remove the house so their nest doesn't fall apart.
The other thing that can start them bar chewing (and this may be part of it as well) is too much cleaning out which removes all their familiar scent. Weekly cleanouts aren't necessary if you have enough substrate in (fill the base almost to the top) and if they can have normal nesting and hoarding behaviours. They will use a litter tray, the rest of the cage mostly stays clean and dry and so you can just spot clean mostly - ie take out the odd handful of substrate when necessary and replace it. You can easily go 6 to 8 weeks or even longer before needing to change the substrate with this method and it keeps the hamster happier. Even when you change the substrate, it's a good idea to replace some of the old substrate that is clean and spread it on top so it still smells familiar (that top layer will gradually get replaced with spot cleaning). And best to only do "partial cleans" - ie don't clean everything at the same time. So just do the wheel as and when necessary, any toys as and when needed at a different time, and the substrate a different time again.
Below are a few options for houses to buy that are good although some are a bit expensive (the rodipet ones but they are very good). Most people paint the inside with plastikote enamel water based paint - a little pot costs about £4. It's pet safe and makes the inside wipe clean so it doesn't get pee stained if they have an accident!
This one is not too big - a good size for a hamster, but not really big enough to fit a litter tray in - that doesn't matter - they'll probably just make a toilet in a corner of the cage and you can put a litter tray there. It needs a bendy bridge over the door as the door is very large. Although it says guinea pig house it is way too small for a guinea pig.
It has no glue or nails, slots together like a jigsaw and the roof lifts off
https://www.amazon.co.uk/Ferplast-Gu...3263384&sr=8-2
This fits very well in the hamster heaven. Same idea as the shoe box house but it has two rooms and two lift off roof sections. You can put a litter tray in the room with the door as they'll nest in the other room which is darker. Then just lift the roof off to empty the litter tray. One roof section is a piece of rough granite so if you put the food bowl on top of it, it helps keep their nails short every time they go to eat (they need something like that or their nails can get overgrown).
https://www.rodipet.co.uk/houses/rod...t-rodents.html
I have this one, which also fits and I think works better if you don't mind a little bit of diy with a saw! It only has a top entrance and it really needs a front entrance as well - so I cut a section out of the front to make a front door as well. I cut out the door in the middle section so there is a room either end of the entrance - one for nesting and one for the toilet. It works well like that and they can use either the top or front entrance.
https://www.rodipet.co.uk/houses/rod...t-rodents.html
This is the plastikote
https://www.amazon.co.uk/gp/product/...?ie=UTF8&psc=1