Usually I use S2 just because I have it fully mastered. S1 could be nice if you get that disorder that forces you to use your moves, or on stages where you need her to not take damage (like maybe high surge versions of the last boss)
Basically you use S2 unless you don't think it'll be used for a high-priority enemy, or unless you think Kroos might die without S1's stealth.
Thanks. I'm probably going to mastery for S2 as well since that's the one I have been using, but once I started looking at her more carefully, I suddenly realised her S1 didn't sound too bad on paper.