Or you can use “comefrom links”, where you in some other file type “<<< foo bar”, and every time you mention “foo bar” in another note it becomes a magic link back to this spot. That serves kinda the same need as tags, but you don’t have to explicitly tag future notes or think about a system of tags, you just wrote normally and automatically get relevant links when you use consistent language. As a user, I feel this is much simpler to use, even though you’re right that Denote itself is implemented in a simple way.
Regarding the GTD system, I’ve also just ignored it ;). If I want a digital GTD I have had a great experience using Org, but these days I prefer a physical bullet journal as it seems to help me ignore unimportant tasks (I’ve always struggled with deleting unimportant tasks - not for technical reasons but for irrational reasons). And since it’s always in front of me on the desk, it’s harder to ignore than the agenda buffer.