Some things to consider regarding the Onslaught.
The Onslaught is ancient. From it's description, we can ascertain that it was designed in a time before shields, having received modifications to get to the point it is at in-game. Already, this means that it's shields shouldn't be up to much, as almost all high tech, shield reliant ships seem to have so little space left for other components that they are limited to energy weaponry. Additionally, design is so significantly different that I imagine high tech ships are built around the various projectors and subsystems necessary to support such defences. As such, the Onslaught's shields should be small, slow, and inefficient for a ship of it's class.
"When first launched from orbital dock, they must have surely dwarfed any other ship in existence"
Further evidence. All this puts the Onslaught at roughly the same epoch as the Hound, a design so outdated that it has either been nearly entirely converted to a cargo freighter, or was built for a time in which hyperdrives were so weak that and even small journeys would take months, or even years.
Note that the Cerberus is obviously a modern(ish) improvement on the freighting capabilities, whether or not originally intended, of the Hound.
Exact sizes are difficult to measure in such an abstract phrase, but this would most probably mean that the standard warships of the time were frigates, with perhaps the rare destroyer or two. The scarcity of low tech destroyers would mean something if not for the possibility that the superior midline destroyers (Hammerheads, Hammerheads, and Hammerheads) completely phased them out before the time at which the game takes place.
As such, the thermal pulse cannons built into the Onslaught are even less sensible than their use on a low tech ship would normally be, as they are clearly not intended for use on small craft.
But do not despair, as there is a (potential) answer to this dilemma. The Onslaught was not meant for ship combat. It was meant for sieges. It was the first step in countering large battlestations, by dumping rounds of thermal lasers at appreciable distance, and then retreating to repeat the process. Additionally, this explains the proclivity for side mounted heavy weaponry - The Onslaught is built to survive swarms of combat frigates as it closes with it's target, breaking the line of battle, and allowing the ships sheltered behind it's heavily armoured bulk to wreck havoc on the enemy. This also explains the burn drive.
Thusly, the Onslaught would have had no issues with the inefficiency of it's weaponry. Of course, it is up to Alex to decide whether the modernisation it received removed that weakness (in this next update, that is).
Anyways, the Onslaught is not meant to be as good as other capitals. The description says it all - it's absolutely archaic, kept alive only by it's simple manufacturing process, ruggedness, and the turmoil and disorder being suffered by the Sector.
