Ah, tricky. If anything, you might have asked why it's not אלה/אלו - the plural forms of זה and זאת, since two and three are more than one.
The answer is that the numbers here don't describe a feminine noun; we're talking about the abstract concepts or quantities two and three. And Hebrew happened to choose the feminine form for the abstract numbers. Each of them is used as singular male.
In addition to your question, I was also wondering why זה instead of הוא? I thought the former was more informal while the latter more formal, but if that's the case is there a tendency to use זה with numbers? Regarding gender and numbers, there is something going on with Semitic languages, because Arabic operates similarly. Some scholars are suggesting that the grammatical genders of numbers are probably historically misleading because they only appear to be gendered, e.g., the t in אחת. If that's the case, then "feminine" numbers being governed by a masculine copula may not be a matter of grammatical gender originally. Here's a link to a blog that discusses the matter: https://www.quora.com/Semitic-Languages-Why-do-feminine-looking-numbers-agree-with-masculine-nouns-and-vice-versa-in-Hebrew-and-Arabic
Good question. I think that הוא sounds less natural here, but I'm not sure anymore if it's not the result of over-thinking it. I just commented on "six is a number" that both הוא and זה sound equally natural, and הוא is a tad more appropriate in formal writing. I'm not sure why the difference, if there is a difference; maybe it's the femininity of שלוש and שתיים that makes the explicitly masculine הוא a bit hard; while in "שש הוא מספר" the masculinity of מספר makes it easier. But not sure at all.