I noticed the 1996 Mercedes S500 has double layer glasses on windows, are they to protect bullets or serve for other purposes?

no standard automobile come s with bullet prooof glass the purpose is for noise control to keep the cars inside interior quiet and serene

run off the mill? no. there are some companies specializing in bullet-proofing cars. it might be some other thing you saw on the glass

This is called "dual paned glass), and it is there to help reduce cabin noise. It isn't "bulletproof."

MB does offer bullet-proof windows on its high-end models for heads of state and gangsters, but those windows are MUCH thicker and most have metal framing around the windows themselves (used to be cars with such windows meant the windows wouldn't roll down at all -- don't think thats the case anymore).