Port Control issues will probably be less since there are no LSA to check and no ISM to be complied with, at least not on board.
One problem is that there are nobody to fight a fire by manual and conventional means, but I would assume that there will be automated system, like water mist for both engine spaces and cargo compartments.
As for Classification Societies they are actively involved in the development o Autonomous ships from the very start.
At least DNV-GL is. Here is their own design for an autonomous short sea ship: https://www.dnvgl.com/technology-innovation/revolt/index.html