"It is a good question."
Translation:To dobre pytanie.
With jest in the sentence, why is it not pytaniem, in the instrumental case?
To and to jest is used in a similar manner. But if the verb is jest (without to), then the noun following takes the instrumental case
Both work, "To dobre pytanie" just seems more idiomatic. It's hard to say though, when the sentence sounds better without 'jest'. I guess it's more like a remark than actually saying 'what it is'.
Yes, that doesn't make much sense. Sentences like "It is Y" are constructed as "To jest" + Nominative.
What if the sentence is "this sentence, or that sentence, is a good question"? Would the object take instrumental case then?
Yes, we have additional context and in fact a different sentence structure, which means that "To zdanie jest dobrym pytaniem" is grammatically correct. Strange though. But correct.