I think the main issue with missiles isn't that Sabot's are too strong.For me,the main issue is that shields are just too damn important,so anything that reliably overwhelms them is bound to be too good.
Shields are the first defense that any ship has,and for the endgame threats(Ordos) its the main defense and largely the only one that matters,their armor is really weak.Exactly the same applies on the Tesseracts.Couple that with the fact that without shields,ships are open to all kinds of debuffs(overloading,weapons/engines disabled) and it's easy to see why Sabots are that good.
Not to mention,even without shields,Sabots overload massively,so they are always useful,unlike an Atropos,that just does a bit of damage on shields and nothing else.
For me,the solution is either reworking how shields work or changing Sabots to have a more long term effect.Instant bursts are always a weakness of shields,especially if the alternative is a massive overload.Also,Pilums are just too slow and fragile to do their work without spamming them,which feels unsatisfying.