Personal opinion: despite being empty and inactive, these comunities are still some sort of a history. And history is not deleted here unless it is strictly against rules. + I haven't seen that admins are able to delete accounts or communities here at all, only ban them.

Why would they?

I see no problem. As a user, I can just sort by most active communities when searching them.

Deleting communities to free server space also means deleting our history, doesn't seem very nice.

Instance admins can appoint new moderators to any community if/when someone wants to take over one of the currently dead ones. That's why many instances have a community_requests community, where anyone can request mod rights for a community that no longer has an active moderator.

It's up to the admins of the instances to delete them, but I think it would make sense to delete them.

There was a lot of communities opened a few years when the first wave of redditors wanted to move everything here. It has a negative effect when people search for a topic and find empty pages and no activity, as it appears as if there's no interest in those topics. It would be better if it was completely empty, so anyone with legitimate interests would feel more inclined to start new ones.