The nonexistent torpedo launcher must be assumed because dialogue established that the E-C could fire torps at evil Romulans. The nonexistent secondary hull ventral phasers won't have to be assumed under that sort of logic...
One might invent a little story that mirrors the real history of the E-C photographic model. Say, perhaps there was an intention of mounting a ventral strip on the secondary hull, the way the E-D and E-E have one across the tummy. But perhaps the engineers couldn't create a convex-curved strip phaser at the time; perhaps only flat strips were technologically feasible. So the ventral weapon was left out, with the intention of installing it at some later date.
The phasers on the engine pylons do offer some coverage. And note how the underside of the fantail changes when the model is altered from E-C to Yamaguchi
et al. - a prominent secondary shuttlebay or cargo hold is installed in that location, where many other ship types tend to mount short aft/ventral phaser strips. Perhaps the E-C style ships had strips there, removed in the upgrade that finally installed the ventral strip?
We may take delight in the fact that the underside of the upgraded model is never shown on screen - so the Yamaguchi
could indeed have had the ventral strip added.
As for the locations of the torpedo launchers, I'd indeed argue for both forward and aft mounts. And since the forward ones are invisible/covered, the aft ones are probably that as well.
In DS9 "Emissary", we see an Ambassador
fire forward torpedoes, plus a forward phaser that seems to come from the underside of the secondary hull. TrekCore has a screencap from roughly the right moment - anybody have better 'caps?
I'd argue for a single forward torpedo tube at the usual bottom-of-neck location, covered with plates in usual operations. It'd be more modern and more capable than the comparable launchers on Excelsiors
, hence the halving of muzzle numbers. On that basis, I'd also argue for just a single aft tube somewhere. There's a curious little round hatch just above the impulse engine that could well serve the purpose - but it's gone in the Yamaguchi