What happens when baker's, butcher's, etc. are in the plural?

Bakers and butchers, in the plural, do not require an apostrophe unless it is referring to something belonging to the bakers and butchers - such as: "All butchers' shops are closed on Sundays."

Your first example is actually an abbreviated way of saying, "The baker's shop is closed on Sundays." Otherwise, it would be "The baker does not do business on Sundays."