My own headcanon is similar to that of a lot of the posts here. The ML-16 was arguably overspecialized against hulls, but neither the GTA nor the PVN had shielding technology in anything more than a very early prototype form (there was mention, IIRC, of a "deflector array" at Ross 128 that ML-16s and MX-50s had serious trouble penetrating).
It was cheap, it used very few resources that required transporting, it wouldn't work for the Vasudans beyond the few that could be captured (due to the weird scarcity of argon outside Sol), it did the job adequately for the era, and it was an incredibly efficient weapon. By all accounts, a weapon that dissolved molecular bonds and used very little energy to do so would've been a godsend to the logistically-strained GTA.
They just weren't counting on enemies who protected themselves with something not based on molecules.
The logistical strain can be inferred in a number of other ways, too. Consider the weapons you start out with on the Galatea in FS1: the MX-50 and the Fury. I choose to ignore the fluff's yield numbers (in megatons) for a variety of reasons, but mostly on the basis of "Sci-fi writers have no sense of scale"
Based on its impact animation, its fluff, and its limited use against shields, I consider the MX-50 to be a glorified shrapnel bomb. Which fits nicely into the "strained logistics" problem, as cheap weapons like that wouldn't need to be transported from Sol -- they could be made
in situ by colonies or even on board Orion-class destroyers themselves. Same goes for the technologically-simple Fury missiles, dumbfire shaped-charge weapons.
