First, double check you don't have the K2 Tools >> Archive (option) module enabled somewhere.

Then simply add a 301 redirect for all /category/date/XYZ URLs to your homepage.

1. It will. That's the point of a permanent redirect.
2. Use pattern matching. I never implied adding dozens or hundreds of URLs.

You can't hack core files to do this cause you don't need to. The entry point for these URLs is the archive option in the K2 Tools module (mod_k2_tools) or perhaps another module from a 3rd party that works similarly. Double verify it's not currently published anywhere. If it's not, the URLs may be left overs from crawling conducted in the past.

Whatever works :)