The 4-bit stuff is a hangover from Notch doing this (I'd maybe even say a similar-calibre programmer to Chris Sawyer...). The sound has nothing to do with technical limits, that's a post-facto rationalisation.
The game never played midi samples, it was always playing "real" audio. The style was an artistic choice, many similar retro-looking games were using chiptune and the sorts. It's a deliberate juxtaposition...
The CPP variant doesn't really perform better anymore either.