I agree, but not in the way you think. For me, it seems like missiles in general have few options simply because a couple of them look to be pretty dominant over other missiles that the player could use.
For AI-controlled ships in the player fleet, it seems like the best choice for small and medium missiles is generally Harpoons. For large missiles, it seems like the best choice is generally Squall, followed by Squall + Locust in a linked weapon group if the ship has 2 larges. This does very well in most of the builds that I've tried. Occasionally, Annihilators or possibly Swarmers will do well as well, and for player control Reapers/Cyclones can also do well, but AI isn't as good about using those.
Conclusion: it is a support weapon for ships outside front line, like carriers. Same role as Pilum. It is not the general purpose kinetic weapon like sabot. In fact, it sucks completely unless you put ECCM and missile spec on it. Otherwise it either never hits or get blocked by the most basic PD set ups. Personally I would not use it very much if I have options for sabot with 2x ammo.
Are you accounting for that the Squall now has scripted anti-shield damage,
precisely because it was doing too much damage to armor/hull in previous versions? So its on-paper DPS is actually 256 kinetic DPS against shields, not the stated 103 kinetic DPS. Even with that, in my testing against double Ordos, the Squall usually ends up doing around as much total damage as a Mjolnir, despite the Mjolnir having on-paper 533 DPS, and usually having the most DPS out of all the large ballistics -- and the Squall does this without using any flux. That's because the Squall gets to hit things from 2500 su away. I don't see enemy PD having much effect against it, and it hits most targets pretty well other than say maybe frigates or something.
I don't see taking ECCM and/or Missile Spec as anything against missiles, I mean we usually assume that the player will be taking ITU and Ballistic Mastery for ballistic weapons too, and many ships that have large missile slots will also have other missile sizes that you'd want them for as well.
The strongest feature of the Squall is how much it softens up the enemy fleet and puts it in disarray even before the two sides engage and while the two sides are fighting, enabling the player fleet to go on the offensive. The second strongest feature is that it enables other missiles linked in the same weapon group, such as Harpoons and Locusts, to be that much more effective by having them fire more often and against targets from farther away. You don't really get those in any other package.