Furthermore, notmuch never ever touches your mail storage. It just operates on tags. It is up to you how to turn tag changes into actions. I find this incredibly elegant and flexible.
I do not tag things manually. I tag incoming messages automatically using searches. Since search is so powerful and quick, I do not really feel I need tags. If you do, mu or mutt/neomutt might be better suited.
One thing I could never figure out with the folderless approach like neomutt is how to make per account compose and responses. In mutt I would set the account based on the folder I'm in and depending on what I'm responding to, but I don't know how to do that in neomutt or rather how to do it when using notmuch in neomutt.
I do use mu4e, which seems to be a bit easier to configure for multiple accounts.
I don't really use tags, but have a few searches to archive email from mailing lists without seeing it in my inbox.
For other usecases, I do as you suggested.
mu using standard IMAP folders means it can interoperate with other mail tools. That's the biggest consideration, I think