in my mimeapps.list file I have zathura set like this:
application/pdf=org.pwmt.zathura.desktop
application/octet-stream=org.pwmt.zathura.desktop;
application/pdf=org.pwmt.zathura-pdf-mupdf.desktop;

I noticed there are two other zathura.desktop files on my system.
~/.guix-profile/share/applications/org.pwmt.zathura.desktop
~/.guix-profile/share/applications/org.pwmt.zathura-djvu.desktop
~/.guix-profile/share/applications/org.pwmt.zathura-pdf-mupdf.desktop

Perhaps I'm using the wrong one here. I also noticed I have two
application/pdf lines, but the first one is from the Default
Applications section and the second is from Added Associations.

Deleting the first line then makes xdg-open use a browser to open the
pdf, so I don't think that's the right way to go.

I tried also copying the later application/pdf line and replacing the
first one in the file with it, so this way it's still in the file in
both sections. With this, the file opens in zathura again, but clicking
links still does nothing. I'm not sure of the significance of the
semicolon at the end. Some of my lines have it, and some don't.

I'll attach my mimeapps.list file in case it's helpful to look over in
its entirety. (file has been reverted to the state it was at the start
of troubleshooting since none of the changes so far fixed the issue)