At the time, it seemed like a good idea, but I agree with you 100%. In 2015, we should definitely be including these in a hak file. But yeah, that'll be waiting for when the hak is redone.

if it were up to me, I'd ditch the whole structure, if possible, and just have a big file, but eh..
Having multiple files with a misleading naming nomenclature has caused alot of headaches... both on player and dev side.