Hi Tomiya,
In the configuration of Value Categories we are defining these based on the Controlling area and not at the company code level. So if your two companies belong to the same controlling area, If anyone creates a Value Category then it will be used by both of them.
There is no consequence of having unassigned cost elements to value categories in CJVC. Only thing is that you will not be able to segregate the cost under some meaningful headings in Value Category reports.. They will fall under the unassigned column. You can still run your cost element wise reports and your reports would be fine.. 
I think here the question is does company B requires reporting based on Value Category? If yes then they also need to create their own Cost element groups and add these to their Value Categories, if not then there is no harm..
Hope it helps you..
Regards
Sammar
Message was edited by: sammar razdhan