Am I doing the right thing for my hamsters? They live in a natural way in social groups but....?

Hmmm, I've never heard of anyone devoting an entire room to their hamsters. Normally most dwarfs do not like very much company of their own kind, they tend to be solitary creatures as they age. But there are always exceptions. I think it is a very good idea that you put them in large tanks at night, if not to isolate them, but just to make sure everyone is accounted for. It's also good that you monitor the breeding because inbreeding is a concern, but you seem to have that well under control. In a completely wild setting without any human interaction hamsters will breed as long as they are able. Typically the babies will leave the mother after a month, maybe a little longer, as they are close to full grown and can eat solid food and forage for themselves. The female may wait a couple weeks before breeding again, she may not. I say as a guess that the most they breed willingly is 12 times a year (or about once a month) but I don't know that they would want to do that all the time, so closer to 6 or 8 is probably what your looking at, at least for a maximum. You said some of them are a few years old, so those are probably done breeding. Since they have so much room to themselves if they want, then I think what you are doing is the right thing, especially if you've been doing it for so long and had no problems. Unless you start to see issues arise (like inbreeding, over breeding, fighting, illness, etc.) I'd just keep doing what you are doing. Being able to roam around this much is good for them, so putting them in cages now would actually probably start fights.