Does anyone know if the issue of not using both hips to sheath weapons but having one just appear is something Bethesda is planning on fixing? Could this be fixed with a mod? Is anyone working on said mod?

Don't think that's something Bethesda is planning to do something with. They made it that way and they got other things to concentrate on. Don't know about the mods.

Seems to me that the best fix would be to put both sword sheaths on the same hip, otherwise the animation for drawing the swords would look wrong.

Prolly something doable with a simple mod, for sword users anyway, just make the sheath on your hip look like two sheaths.

Other combinations of weapons would be difficult though.