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あれは何ですか what’s that?
今何時ですか what time is it now?

I learnt these two sentences from a Japanese learning app. I am confused why the first sentence uses は whereas the second doesn’t. The English translations are both in the form “what is...?”

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The first point to make is that the first sentence can work without the は (though it’s slightly informal to drop it) and the second sentence can work with a は (though it’s more common/natural to not have it).

That said, there is probably a difference in the grammar, which is that あれ is functioning as the topic in the first sentence, while 今 is functioning more adverbially in the second sentence (similar to how the “right now” in “what time is it right now” works). Perhaps due to this, usage of は in the second sentence feels like it has some sort of extra nuance, like contrast. That said, in a very formal context I feel like people would include it regardless (perhaps as a form of hypercorrection?).

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あれは何ですか means "speaking of that, what is it?" Here, は indicates that the previous constituent is a topic of our discourse: we're saying we're talking about that over there. Japanese doesn't need to have the topic in every sentence; if you don't say it, it is assumed you are continuing to talk to whatever the topic was before, or that it is completely understood what the topic is. If you just say 何ですか "what is it?", in absence of a previously established topic in both English and Japanese the most natural response is to ask for clarification of what the subject was: 何が...? (or "What is what?"). But if someone points out a thingamajig and tells you they want to buy it, 何ですか is perfectly natural - you already know you're talking about the thingamajig, and re-specifying the topic with あれは is unnecessary.

今何時ですか means "what time is it now?" without any specific topic - it is a very neutral question, with all the information already present, and nothing missing. If you just ask 何時ですか "what time is it", either you have already talked about something (e.g. a friend's wedding, in which case the sentence will mean "what time is the friend's wedding?") or it will mean "what time is it now?" simply because it would be stupid to say "what time is it" out of the blue and expect someone to know you're not talking about anything but now.

You can topicalise pretty much anything (except question words) in Japanese. Thus, 今は何時ですか "as for now, what time is it?" is perfectly fine. It does gain a slight contrastive meaning (like if you asked five times in the last ten minutes, and you're asking yet again - "what time is it now?")

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