Question: What is the difference between the letters ס (Samekh) and שׂ(Sin)? Did they ever have different sounds?
Answer: In modern Hebrew there is no difference in sound between the Samekh and Sin. English pronunciation for both of these letters is S as in sun. Exactly like in English there is no difference in pronunciation between “sent” and “cent”.
Predictably the Samekh and Sin sound the same in different words, and probably the most astonishing example is the spelling of הִשְׂכִּיל and הִסְכִּיל (both of them are read “hiskil”). The first word means “he made understood” or “he made clear” whereas the second word means “he acted foolishly.” Cases like this one along with some observations of the ancient spelling allow some scholars to suggest that it is possible that before the Exile the Samekh and Sin sounded distinctively different.
This theory may be strengthened by the fact that another pair – ט (Tet) and ת (Tav) had distinct sounds in Ancient Hebrew. Tet was pronounced like a T in toy whereas Tav likely sounded like a combination of letters T and H in thin.
As Hebrew students we should appreciate these simplifications because they make the reading process much easier. The main thing is not to "act foolishly" when it is intended to “make something clear.”