Learn Spanish (Latin America): Hay once niños y doce niñas en la escuela. - There are eleven boys and twelve girls in the school.

No, they do not! Unlike adjectives, numbers like once (eleven) and doce (twelve) stay exactly the same whether you are counting masculine nouns like niños or feminine nouns like niñas. The only number you have seen that changes for gender is 1 (uno, which becomes un or una).

Why do we use hay for 'there are'? Does it change if there is only one child?

Hay means both 'there is' and 'there are'. Unlike English, which changes the verb depending on how many things you are talking about, Spanish keeps it simple! You use exactly the same word whether there is one item or a dozen.

I learned that niños means 'children'. Why is it translated as 'boys' here?

You are right that a mixed group of boys and girls is just called niños. However, because this sentence specifically contrasts them with niñas, we know that niños refers exclusively to the boys here.

Does the word en mean 'in' or 'at' in this sentence?

It can mean both! The Spanish word en is very flexible and covers 'in', 'on', and 'at'. So en la escuela translates to 'in the school' or 'at school' depending on what sounds most natural in English.