Update 23/06/2017: if you came here looking for solutions to Autoptimize cache-size problems after having (been) updated to AO 2.1.1; there’s a bug in that specific version, please update to either 2.1.2 or to the most recent stable version (currently 2.2.1).
Copy/ pasted straight from a support question on wordpress.org;
Auto-deleting the cache would only solve one problem you’re having (disk space), but there are 2 other problems -which I consider more important- that auto-cleaning can never solve:
1. you will be generating new autoptimized JS very regularly, which slows your site down for users who happen to be the unlucky ones requesting that page
2. a visitor going from page X to page Y will very likely have to request a different autoptimized JS file for page Y instead of using the one from page X from cache, again slowing your site down
So I actually consider the cache-size warning like a canary in the coal mines; if the canary dies, you know there’s a bigger problem.
You don’t (or shouldn’t) really want me to take away the canary! :)