Yes, autonomy underwater is the biggest issue. Its an issue even for USV, and there the basic technical challenges are far more trivial (the operational challenges in a contested environment are something else).
Torpedoes use wire (fibre optic) guidance for the same reason. In fact any breakthrough in underwater communications would probably have far more immediate repercussions for how torpedos and missiles can be used as opposed to controlling UUVs.
For the time being UUVs for reliable communication either need to rely on wire guidance like torpedoes or they have to deploy an emitter to the surface, and a crewed submarine would have to do the same. With obvious issues for detectability.