in The Arsenal of Freedom, the torpedoes fired out in an arc along the plane of the launcher.
Indeed - an extremely acute arc. Had they simply kept on turning that way, they could have headed in any direction they pleased. And there's no good reason to think that a torpedo that can make a sharp 50 degree turn couldn't make
a) a sharp 550 degree turn or
b) five hundred consecutive 50 degree turns.
So torpedoes have amply demonstrated the ability to head in any desired direction, making the direction of the launch tube quite irrelevant. For example, Kirk in "The Changeling" shoots over his shoulder, ordering a target at 123.18 to be hit by a torpedo from a forward
tube (as confirmed by the visual of the departure, and the dialogue reference to #2 torpedo, which was among the forward tubes listed in "Journey to Babel" along with #4 and #6).
My knowledge of New Ground is lacking, so to that point I cannot speak.
Shields at 12% encouraged our heroes to fire yield 16 torps at a range of 23 kilometers, but they were being too optimistic and suffered major damage from this.
We don't know what yield 16 means - is it a lot or a little? Yield 5 was a little in "Redemption II", but that doesn't help much since we never heard what yield 1 would mean. What our heroes were trying to do was to disperse a shockwave capable of shattering a planet, though, so "a lot" would make more sense than "a little" in the context.
In any case, the whole battle in "Jem'Hadar" took place at ranges much shorter than twenty clicks, and would probably have blown even fully shielded runabouts to smithereens from the possible hits on Jem'Hadar ships.
we've never seen the torpedoes strike a target to the side of their ship
We were told that this happened in "The Changeling", and we saw a hit that was actually better than that in ST6...
That The Enterprise weapons systems were fully functional I have no doubt.
Why? The ship was being blasted to bits, so loss of weapons would only be a natural assumption. Indeed, Riker ordered a spread of torpedoes to be prepared for the final desperate attempt to destroy the Duras sisters, but when Worf hit the trigger, only a single torpedo was fired from the aft tube...
A small bit of dialogue from Worf or Data saying shield control systems were off line, could have been the thing that kept the Enterprise from rotating her shields frequency while the BoP could keep rotating hers back and forth as she fired.
Why should we assume that shield rotation would
a) help at all against an enemy other than the Borg, or
b) not be taking place throughout the battle?
Every time the E-D rotated shields, it would be LaForge rotating them, and telling the Durases the new setting.
We have seldom heard of any opponent adjusting weapons frequency to penetrate shields, supposedly because it's impossible to know the shield frequency of the opponent unless one has a traitor aboard. But shield rotation at best keeps the enemy from utilizing a weakness. It doesn't increase the overall strength of the shields beyond their natural maximum. The BoP had feeble shields according to all the experts in the movie, on both sides: both the Klingons and the Starfleeters were convinced the ship could offer no resistance to the E-D. When it did, then, something must have been changed by some unexpected agent. Soran is the obvious suspect.