1. Munchkin talks to Marketo's servers, but not vice versa. So there'd be no way for Marketo to know if Munchkin.js is loading on a website that hasn't gotten any hits (in the past 90 days).
2. I don't know of a manual cleanup, but it should clean itself up as activities are purged (although I don't know off the top if the index is preserved even after 90 days). Maybe you could ask support to do what amounts to a reindexing.