It's something we went back and forth on very early on, and the Onslaught is one of the first batch of sprites, so it had those weapons baked in - but they just never got replaced with proper hardpoint mounts, and the idea was never resolved either way.
It came up again when implementing systems - some are done as "weapons" under the hood, for example the flare launcher - so that naturally brought up the idea of "weapons as systems". But that's actually pretty awkward, both from a UI and an AI perspective. So it just felt right to add these - so there's a proper way to do something that's now so natural to want to do.
The Onslaught was a good candidate - it could use the boost, and those two hardpoints are the least useful large slots on it. Even more importantly, it adds extra personality to what's a very important ship. (The reason they're energy, btw, is so that having them doesn't skew the kinetic vs high explosive choice for the rest of the mounts.)