To elaborate, the sabot shot is very effective against shields (due to being kinetic) and has high enough damage that they can easily punch through 200~ armour - the typical amount your average frigate has. That they fire and reload in three-shot salvoes as well means that a frigate without serious shield efficiency or armour is going to take a nasty amount of damage.
Harpoons are, for starters, much slower. They also deal explosive damage, which shields are resistant to. You can get a similar effect from them, yes, but that requires the target to be on the verge of an overload already. Sabots can overload frigates (and destroyers with weak flux/shield) from zero flux.
The counters to a sabot salvo is either being close enough that PD takes out their first stage, or being so far away that the second stage doesn't fire. The AI doesn't know to do either of these things, and I've lost ships to them as well simply because there's very little time to react.
The same is true with vanilla sabot racks of course, but it's made far worse if it can be done repeatedly.
(Doing some testing; reducing the cooldown to 4, reload and burst size to 1, prevents that without making the small sabot rack underpowered.)