From "Elaan of Troyius":
KIRK: Chekov, arm photon torpedoes.
CHEKOV: Photon torpedoes ready. ...
KIRK: ... As he passes, I want to cut in warp drive. We'll pivot at warp two and bring all tubes to bear. ...
KIRK: Mister Chekov, give him a full spread of photon torpedoes.
It doesn't say whether a "full spread" consists of 4, 6 or 8 torpedoes, but "all tubes" suggests indeed at least two torpedo launch tubes and - given the context - discards the possibility of an aft launch tube as this would be included in "all tubes".
If the "Journey to Babel" writer wanted to suggest launch tubes 2, 4 and 6 why didn't he write so
Fire "torpedo tubes 2, 4 and 6" would not have been ambigous and everybody in the audience would have understood.
Instead, the dialogue only refers to numbered photon torpedoes and IMHO suggests that torpedoes 2, 4 and 6 had a yield that's different from torpedoes 1, 3 and 5 which is the reason why Kirk specifically wanted to have those fired.