Yeah, that's likely very true for a lot of the more localized music zines. Some punks took preservation seriously early on though. For a while, a website called Operation Phoenix had a sizable chunk of both Maximum Rock-n-Roll and Flipside (which was incredibly useful). And someone has all of Slash up too, online. And I want to say that MRR used to be up on their website - at least some issues? You can order many back issues of MRR from there. Oh, and I do have the complete run of The Big Takeover. You can just order it from Jack Rabid for like, a couple of hundred bucks, I think it was.
There are several zine libraries, with the biggest collection in an academic archive being at Barnard. the local non-profit libraries tend to only have local stuff. So some stuff has been preserved, which is great.