Each of the sentences you wrote is correct. The meanings are just slightly different.
1. "Now, you may ask why I wouldn't include this topic in the research..."
2. "Now, you may ask why I won't include this topic in the research..."
In #1, "would" could be past tense, but I think the more natural way to read it is as a subjunctive, as in the sentence, "Why would you do such a thing?" It implies a hypothetical circumstance (even though we know that the circumstance is true). You're saying, "You may ask why a person would make the choice that I've made (to not include this topic)." You are about to answer this hypothetical question about why someone might choose not to include this material. We know that the answer to the hypothetical question ("why wouldn't you?") is also the answer to the more direct question ("why didn't you?").
#2 is more direct and sounds a bit more firm. "I won't" sounds like an absolute refusal, so the question isn't just "why would I, or anyone, choose not to include this topic," but rather, "why do I choose to explicitly NOT include this topic."
The basic meaning is the same: the topic is not included in your research, and you're explaining why it isn't. The emphasis is just a bit different in each case.
(Sorry, I ran out of space -- I'll add the rest as a comment under this answer.)