I am a big fan of the hot questions list. I look through it almost daily to see if there are any interesting questions. It's purpose is (at least in my mind) is to show the top questions thoughout the Stack Exchange network. It would defeat its purpose if it excluded some sites.
Consider that many people have different varieties of interest than you do. Some programmers are interested in the top questions on the Christianity site, and some cooks are also interested in math. Removing "irrelevant" sites from the hot questions list would likely upset more people than it would help anything.
That said, I can relate to not wanting to see questions from particular sites. For example, most of the gaming questions that make it up to the top of the list relate to games I've never heard of before and don't care about, and most of that math questions are completely incomprehensible to me. Even so, there is the occasional gaming or math question that I think is interesting, and if those sites were blocked from my hot questions list I never would have seen them.
If you only want to see the hot programming questions, you can click the "hot" tab on the Stack Overflow questions list. Same for Cooking, and every other site.
This is a feature that would be complicated to implement (Who considers which sites are relevant to users of other sites? What about people who use multiple sites?), would not really provide any benefit, and would upset cranky people like me.