Yeah, they can’t be hive mind otherwise that’d be no fun. I quite like the idea that even though the twins both “hear” the same thing, they react differently. So Tsume telling Shikako that Kiba would make a good boyfriend would cause confusion in ever-oblivious Shikako, whereas Shikamaru would hold a heretofore unseen grudge against Kiba for a while.
I suppose for the short term “find the ferret” mission, both twins being sent would make sense–they can cover a larger area faster and with instantaneous communication–and would be a good first command mission for new chuunin!Shikamaru and Naruto (although, given the bond, would that have pushed Shikako’s almost promotion due to strategizing into an actual promotion?) So that covers the Gelel arc.
But I don’t see why they would both be assigned to the longer-term semi-diplomatic mission to Land of Moon… Or, rather, that they would both be assigned, but only one of them would physically go while the other stays behind to act as Intel handler.