I have used Zettlr a lot in the past and switched to Obsidian for my general work notes. Both retain the folder structure and would fit your needs for hierarchical organisation. Just load your desired folder as project/vault and you are done.

Obsidian has better backlinks and tagging workflow and a lot of nice plugins for productivity.

Zettlr dev states it is for (academical)writing and therefore will not focus on productivity features.

For Projects I prefer Logseq, as it creates a natural structure very easily and fast. The downside for me is the non standard markdown.