I don't know.
> Did he even have a warrant issued to him related to these documents?
Yes. A zine put together by a group that later goes on to commit a crime together, that promotes the ideologies underlying the crime, feels like the kind of thing a search warrant/subpoena would apply to. The fact that the person involved in the crime asked that they be hidden makes it pretty obvious that they saw it that way as well.
> Are these zines even relevant evidence?
Yes.
> Is everyone who has these magazines also now a criminal?
No. Things can be legal and evidence of ill intent at the same time.
> What about other radical anti-government political pamphlets like Common Sense?
If the editor(s) of that pamphlet went on to commit a crime of a political nature, no doubt their relationship with the pamphlet would be evidence used against them. It would also still be perfectly legal to have, and legal for others to continue publishing.
> Seems like quite a different thing than moving some political pamphlets.
It is, but I think the core idea of involving yourself in the crime by way of trying to hide evidence etc. is similar at least.
> What's the relevance again for the ownership of political pamphlets to committing crimes?
Depends on the crime. If they had robbed a Wendy's, probably no relevance. If they attacked an ICE building and the pamphlets established ill intent toward ICE, probably a lot of relevance.