When I looked, I didn't find any renewals for anything referring to the Spirit, and very few of the original inserts carry a copyright statement at all. Granted, that's not 100% conclusive, for a variety of reasons, when it's every single issue over an extended period, the probability of a misfile is pretty low.
If anybody has an idea on where to look beyond "I think he would've done it," I'd be glad to hear it and check it out when I have time. But based on the CCE renewals, if Eisner or his estate were/are blocking people from reprinting the issues, it's not because of copyright.
Also, keep in mind that there's no legal problem with claiming you own a copyright on something in the public domain. And prior to all the records being put online, what layman would dare challenge a Cease and Desist from Will Eisner? The common wisdom has always been that the creators would know better what they do and don't own.
I'm not saying he was defrauding people, by any means. But I am saying that, for example, if he mistakenly confused copyrights with his trademark, no fanzine would challenge him on it. That doesn't mean he had standing, though, if he took it to court.