So yes, these two characters often did collaborate in the comics, though Stephen Shin frequently played a complicated role in the struggle between Aquaman and Black Manta.
Though, if and when Aquaman 2 takes place, it seems like Shin will very clearly be working against Aquaman, and assisting Black Manta.
Stephen Shin is not a clear-cut ally for Aquaman and Mera.
The villain often used Shin as a pawn to manipulate Aquaman, and there are times that Shin — though mostly loyal to Tom and Arthur Curry — betrayed the King of Atlantis to satisfy his own need for more knowledge about the underwater kingdom.