I really like Calibre, but it's tag system is pretty clunky. I don't think I can even tag multiple books at once.

It's definitely clunky, but you might like to know that you can tag more than one thing at once:

Select more than one book, right click -> Edit metadata -> Edit metadata in bulk

Not only can you have multiple tags, you can have icons which are conditionally displayed based on tags. Tags are stored in a single metadata file, one directory per ebook, so can be parsed with a script when performing bulk operations.

You can then customize search engine like recoll to display ebook metadata as contextual snippets in full-text search results. Best of both worlds.