The first one is unlikely. It's emphatic and I don't think the Italian conveys that. For the second, there's no reason why the progressive in English couldn't correspond to the simple present in Italian. It was accepted, in fact. There isn't a one-to-one correspondence in usage to similar verb constructions in different languages.
I agree with the use "how many OF THE boys" because it makes it clear that you are referring to a specific group, whereas "how many boys eat fish" could be seen as a global question...!
maybe because it is a question that would be asked when someone is cooking dinner for boys, and they need to ask how many of them eat fish? i'm not 100% sure, but the sentence implies that boys aren't presently eating fish. So I think i may be right, sorry if it sounds confusing. :)
In addition to Howard's answer: some questions need do, some don't. Here's a very complex explanation when "do support" is needed (first answer):
Can someone write the difference in word order between the two questions of:
How many boys eat fish? Vs How much fish do the boys eat?
I almost tried to do the second one but did not have the word choices available, so I clued in to the first question as the correct answer.