AF performance isn't too different from the k-3 in low light. If it's extremely low light, the green led will illuminate the scene. I never saw problems with the k-s1, even in pretty ropey lighting. The high ISO noise performance is slightly better than the k-3, but they are fairly similar. The main difference is that the noise on the k-s1/k-s2 has a nicer look to it - so if your max on the k-3 is 3200, you might be ok with how the noise looks at ISO4000 on the k-s2. The biggest difference between the two is the additional colour information from the 14bit k-3, and it's slightly nicer white balance performance, makes it easier to get accurate colours in Lightroom for those nasty low light shots.
Tl;dr, I'd still prefer the k-3 over the k-s1 for low light, but the noise of the k-s1 is slightly nicer at say ISO 6400. Beyond that, I'd still prefer the AF of the k-3, but even with its 11 points, the k-s1 isn't too bad (I certainly had no trouble with it). The k-1 is a huge improvement in low light, the k-s1 is a slight improvement.
Here's a not very useful, and somewhat unfair comparison between the k-s1 and k-3 at ISO1600
K-3 + FA31:
https://flic.kr/p/CVQBit
K-s1 + DA35 f2.4:
https://flic.kr/p/CVQBi8