Well, they do? Sodium, for instance. It's a mod, not a full rewrite, rewriting the client from scratch would mean a lot of boring work like speaking with Mojang's server, but I understand Sodium basically rips out and replaces the entire graphics pipeline of the client.
There are tons. There are mods that rewrite graphics rendering, chunk loading, multi-threading, ...
Yeah, it was always weird how 32x32x48 extreme reactors lagged the game whenever you looked at them, but the moment you looked away everything was fine.
Ever since I started playing it in the beta days I've been frustrated with how poorly Minecraft performs relative to what it's showing on the screen. (Not that that stopped me from pouring hundreds of hours into the damn thing.)