Kinetic rounds are less effective against REACTIVE armor per-mass/accelerant than payloads of shaped explosives of the same mass. Against a solid plate armor it makes sense that a kinetic shell will do more damage but SS vessels aren't using solid plate armor, they're using
IE if you fire 100 pounds of kinetic shell at a ship with reactive armor, your round will do 0 damage to the insides of the ship & wipe out exactly 100 pounds worth of reactive armor, while also expending 100 pounds of accelerant getting your kinetic round to velocity, meaning you've expended more than the defending ship.
If you fire a HEP payload that has enough explosive compound packed in to generate the explosive force of 100 pounds of kinetic, because you're using shaped chemical rounds which detonate at point blank range you're actually firing smaller shells than the force-equivalent kinetic round & triggering (disabling) the same amount of reactive armor, using less shell and accelerant in the process.
The drawback is that HE doesn't work in a vacuum so it'd only maintain peek efficiency when striking a solid, malleable surface (armor) and otherwise, without an atmosphere helping contain the explosion, blows the explosion out into vacuum, hence it being best against armor and worst against shields (in vacuum) and hull (no solid striking surface)