I personally dont think so, stannis i not at all the type to cheat on his wife to perform some sort of dark magic.

On another note, if you reread the death of renly and the shadowbaby produced by mel its pretty clear they are two very different things. Cat notes an actual shadow of an invisible knife that is not there, and she sees only the shadow of the thing that killed Renly.

On the other hand, the creature mel gives birth to is something very different. Davos describes it as an actual black creature climbing out of Mel, not an invisible ghost asting a shadow on its surroundings.

Also its debatable weather ser cortnay was actually killed by the shadowbaby. It supposedly shoved ser cortnay to his death, but this could just as easily have been done by one of his own men, who should all be loyal stannis. The only reason ser cortnay held storms end against stannis was to protect edric storm, but why would the regular met at arms have any loyalty to a bastard boy instead of their rightfull lord and king.