Consider this question: https://mythology.stackexchange.com/q/61/33
It's probably the case that no two sources are going to agree on how tall Hercules was, or how many cows he could lift, or whatnot. Should we, then, deem these questions off-topic?
I wouldn't close them as off-topic. I think comparing the different sources and determining which one is more reliable (or why are different versions equally valid) would also be interesting. What I think would be the ideal outcome for those kind of questions is a community wiki answer with the most interesting sources referenced and summed up in a relatively concise way (probably taken from several answers posted previously).
I agree with AI.R's answer - if there can be a valid comparison made between several sources, it's still an interesting question.
I just wanted to add a comment in the case of this question specifically: I believe it's trying to ascertain whether Hercules was man-sized (but tall for a man), or going in to the realm of giants. Although a question asking his precise height would be pretty unanswerable, and would therefore not be on-topic, trying to ascertain how his physical characteristics (as a demi-god) differ from mere mortals could be a valid question, potentially answerable from a variety of sources, and should be encouraged.
What should we do with questions that probably have different answers in different texts?
Unless it is something so precise it varies between every single texts, I believe we should try to acknowledge that it varies, and ascertain how the aspects are varied between stories and versions. It may be that an overall consensus emerges from this.
On the same topic, I answered a question about Arthurian legend, where every account differs somewhat. I thought it a very interesting question and took an approach similar to the one suggested above (comparing the sources and concluding that there is no final answer), and would be interested to hear your opinions on whether this approach is successful. If you believe it is not, I'd like to know if/how it can be improved.
I would say that usually when two sources disagree, it is because not everyone believed in the same thing. The bigger the extent of the culture, the more there will be some small differences on depending who and when you ask. It becoms more or less a sub-myth, like the greek and roman mythos which are close but not identical (and it's not only about the names).
I would probably say a question asking which one is true might be off-topic when not everyone even back then agreed on it. It is not history so there is not really a "true" version. I do think it is interesting to ask who believed in this version and who believed in that version.