notmuch is objectively worse if you expect your email tags to be synced via your mailbox, which I don't see a reason not to expect. Mu uses a header in the mail, notmuch uses a separate database. Other than that point, as far as I can tell they are identical.
I sometimes destructively wipe my machines and I enjoy knowing my email is separate and I don't have to faff with my tag database backup. That said, I do also use multiple workstations - which it is also useful for.
I'm not very much into Mu. I prefer Notmuch as I find the TUI more elegant and it's completely oriented towards tags and searches. Mu also supports folders, and that made it a bit more complicated to me.
