I used to consider sabot missiles as a disgusting - surprise attack - hard to counter - burst damage weapon. But, looking back, that most certainly was the reaction of an unexperienced player that didn't like loosing ships to these "surprises".
In fact, I think my everlasting love for LRPD comes from my fear of sabots, and the LRPD's ability to act as a sabot spotter / catcher (to a limited extend, granted).
Nowadays I'm OK with these and all other ammo-limited vanilla missiles.
Do they have a significant impact on balance? Yes.
Is it a bug? No, it's a feature. (sorry, couldn't resist)
The point is, those missiles help making battles less predictable and shorter. They help most ships to shoot above their weight. Looking at the big picture all of this contribute to make Starsector a better game, IMO.