good point ! i personally have separated it from my resources which is my more active and important stuff, with the remaining resources being part of "My Maps of Content". You can see an example here https://publish.obsidian.md/johnmavrick/My+Resources/My+Resources
and resources is for the main topics, not for every single information-related note you make, those go into the root folder.
but then the same problem would happen in My Maps of Content. right now i have the query set to only show resource notes i have not made links to from the "My Resources" note, so i can use it to still see all of them.
it will not be unusuable because in the "My Resources" note you can set up related queries like seeing which notes have the most links, the most words, etc, as well have a manual linking of the things like I do in mine. does that answer your question ?