Why does towing pods decrease ship acceleration?
Chuck has a part of it. A tractor mount can take only so much before it fails, hence the total strain you put on one must be controlled. With smaller numbers of pods, you can spread the strain between multiple tractors and thus sustain higher accelerations without wrecking a portion of your ship's hull and shedding pods. As for the LACs in HotQ, remember that it was necessary for the Peeps to use sufficient tractors to completely "zone" the LAC. This was to insure that all portions of the LACs' hulls accelerated at the same time and rate, but it was also to spread the strain on the tractor mounts.
Even more importantly, however, towing pods astern requires a tractor link through the open after aspect of the wedge. The more pods there are, the wider the open aspect has to be. The wider the open aspect is, the less efficient the impeller wedge is and the less efficient the inertial compensator becomes. As the inertial compensator becomes less efficient, the max acceleration to which you can take the drive without risking compensator failure drops. The sheer power of the drive is also a factor; you can trade off brute power for impeller wedge efficiency to a point, which is why the Peep Mars-class CAs, with humongous drive power but less efficient compensators, can tow more missile pods than a Warlock-class [I believe he meant Star Knight-class - Ed.].
I think from the above you can see that stowing missile pods internally will not have the same deforming effect on the wedge that towing them astern will entail.
Take care--David (vanishing back into his literary slave labor camp)