Check out this program, @psophos. Neither open source nor totally free to use, but is probably what you want. Sorry for the link to some other software))
On the original question. I got Inbox folder to store things I am not sure where to put yet. A Wiki folder with a bunch of sub folders on topics. I also got Contacts (yes, I do store some of them in Joplin). And I got a Diary folder with pages named like 2020-01-07 under it.
I do think that structured (hierarchical) tags could help categorization in Joplin A LOT making it one of the best software in any list. If you do too, please upvote the issue (or even help with it if you got skills).