But that's the POINT of the Sabot - either overload the enemy ship, or force it to drop shields so you can whack it hard with HE or EMP. It's not really supposed to be a conventional finisher like a Harpoon or an Atropos. As it stands the weapon is almost too versatile, and the only reason it isn't completely broken is because that first stage of the rocket is so slow. If it cost more OP I could understand it as an "all-rounder, doesn't matter what you use it on it'll die" sort of weapon, but as it stands it really should only be a shield cracker / frigate crippler.
Two reasons why Sabot is not overwhelming: One, first-stage delay. Sometimes, you only have a moment and Sabots are too slow to take advantage of that opening. Two, AI sees Sabot as anti-shield and wastes them mostly on shields instead of saving it as an unblockable finisher. If you want to give AI missiles, it is usually better to give them Harpoons (or Annihilators).
I would not want to use missiles solely as shield-breaker. Shields regenerate, Sabots do not. Old default Hammerhead configuration with Sabots for anti-shield and Assault Chainguns for general-purpose assault was a joke.
A few versions ago, Sabot had a shotgun-like spread which did even more damage to shields than the original and current Sabots. The fatal problem was the AI always dropped shields and took insignificant damage to armor and/or hull. This meant the only one who suffered the extra shield damage were likely ships piloted by less competent players instead of the AI. Shotgun Sabots was only useful for forcing the AI to drop shields, which might useful if the missiles were unlimited and the ship has superb burst damage configuration (such as multiple blasters or plasma cannons).
Today's Sabots are brutal and effective. I like them, but not enough to use them unless they are free (i.e., 0 OP one-shots).