Ex ante (before the fact) vice ex post facto (after the fact) is the better way to do it. Ex ante changes are ones done beforehand, often with the intent to drive a theme or play experience. These are generally good, as the players can anticipate the effects and play accordingly. If, however, you're changing the baseline of your campaign because of player build choice, that's ex post facto and reduces the expected outcome of player choices in a way that the player cannot predict. IE, if you adopt selecting higher ACs in general to offset the player choice of SS which makes lower ACs less viable, then you've changed the game from the one the player made a choice in to a different game where perhaps a different choice would be better.
Further, by making the change ex post facto, your still doing it for balance reasons, only you're hiding it from yourself. A decision to change the rules to level expected outcome prior to play is far better than a decision that changes the baseline assumptions of the game to control the effects of player choices after those choices are made. Rule wise, at least. So, if you're choosing to outfit humanoids with better armor because the CE SS archer needs a better challenge, that's metagaming ex post facto, and IMO a poor choice. If humanoids start wearing armor because the CE SS archer convinced the party that the humanoid raids on armor shipments wasn't worrisome, that's not ex post facto, that's consequences. There's a difference and it's important. Changes should evolve in the fiction due to player choices in the fiction, not because the mechanical choices mean you feel the need to balance things.
Given that a standard response to complaints that SS is unbalanced is to suggest ex post facto solutions, I think people aren't putting enough thought into it. Upping ACs to offset SS is just like having a bunch of fire resistant critters show up all the time because your mage likes fire spells. Every now and again, as it makes sense in the game, this works well, but as a solution to an issue it's bunk. You shouldn't be in the business of punishing player choices because it's easier than looking at rules tweeks beforehand.
So, if SS is an issue, (and I think it is small one), the better response is to discuss how to make a change before play rather than take the player punishing route of hiding the fact that your correcting the issue by picking more critters with high ACs.