I believe sometimes it’s done because there’s a lot to read and it might be (considered) too hard to read in real time. Which I understand, but it also annoys me too. It’s not what they said, and sometimes the way someone phrases something is important even if they don’t cut out important information, it can hint at their character or their emotion.
I’m not sure why subs would be so weird and verbose. Maybe the translator is afraid the implication (rather than literal meaning) will be lost somehow, but really, ‘ja’ isn’t some loaded enigma.
On a side note, fan works (anything from subs to software to upscales and remasters) tend to be better, done out of passion rather than just an industrial chore.