The off-topic boundaries here are poorly defined in general. Whether a question attracts votes to close is sometimes a matter of who happens to be online at the time. I prefer to err on the side of inclusivity when we have uncertainty.
How does the Zamzam well never run out of water?
I'd consider it okay to ask:
It's possible this is viewed as a miracle in Islam, in which case it is definitely on topic.
Even if it were purely a request for science, it's still an Islam-related scientific question. Other requests for science include:
(+4/-0) How is it possible that the coccyx does not decay at all? What if the body was cremated?
(+2/-0) Masturbation is haram but what is the scientific reason?
(+5/-0) Biology In Islam - Reproduction
(+3/-0) Do the Scientific Miracles in the Qur'an actually exist?
(+5/-2) Isn't this hadith about sunset unscientific?
(+5/-1) Is there any mathematical patterns or logic in the Qur'an?
Moreover, having a scientific explanation for what could be (mistaken for) a miracle seems helpful for understanding Islam.
Should questions about Islamic sites such as Masjid al Haram and the Zamzam well be asked?
The rule of thumb I proposed here is: if it helps understand Islam, it's on-topic. And, if there's any doubt, the author can indicate what they intend to learn about Islam from the subsequent answers. To illustrate:
What's the distinction? For the Somme question we don't learn about Islam, whereas for the Camel/Karbala questions we do learn about Islam.
This likewise applies for Arabic language questions, questions about other religions, questions about culture and behavior.
Here's some examples of questions about specific sites:
(+12/-0) Why is the Kaaba covered in black cloth?
(+5/-0) Why masjid Haram is called that name?
(+5/-0) Are Mecca and Becca the same places?
(+3/-0) Interior of Kaaba
(+2/-0) Where did the Prophet's hair in Pakistan come from?
(+2/-0) Where was Muhammad al-Baqir(as) during the Battle of Karbala and what followed?
(+1/-0) Did Iranians fight in the Battle of Karabala? (As Imam Hussein's soldiers)?
(+2/-2) What proportion of graduates from Al-Azhar University are female?