Is it composed of “で+は“ while は just highlights the noun before it? But if that’s the case then does 授業 here refer to a period of time?
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授業 does not refer to a period of time, but rather the class in general. The second sentence translates as "The history teacher is Japanese, and rarely uses English in her classes." The では is frequently used in negations, but particularly where you are stressing the modifier vs the verb:
In verbal English, you could stress Shinjuku to produce the second meaning, Implying that you might shop in other places which are not Shinjuku. The first sentence might imply that you do other things in Shinjuku, just not shopping.