I will be commuting from Zug to Winterthur for (initially at least) a few weeks and am wondering and if anyone else is doing this and could tell me how full trains are in the morning and evening.

Is it normally possible to get a seat? (in second class)

When is the best time to leave Zug so that I would encounter a lower number of rush hour commuters?

I would say there are more people commuting into Zug than commuting out, so you should be fine anytime.