EDIT: D3rr have offered a possible technical solution I'm very happy about. Thank you for your time.

It's just an artifact

No doubt, but not doing anything will:

An example would be /s/Archeology. It's currently inactive (1 post last 3 monts), yet it's one of the top 3 subs and will continue to be so until you change the mechanics of auto-subscribe and current subscrictions OR somebody starts shitposting to the point where people unsub en masse.

might make new users not be subscribed to everything.

considerthefollowing.jpg:

If you stop auto-subscribing for new users, there will a 5270 subscriber difference between a new sub and the oldest, inactive sub. I believe a common way new users from reddit-like site finds new subs is to sort by subscriber count and pick as you go down until you reach a personal threshold size.

This is unfortunate in two ways, it stifles the growth of small subs and users who subscribe (or alternatively 'don't unsub from') /r/Archeology will find a ghost town with 5000+ inhabitants.

We have no plans to change people's existing subscriptions

If it's possible from database info, how about autosubscribe all users to subs created after account creation and keep auto-subscribe then? It won't have to change the current system, yet will reflect the actual community posting grounds?