In terms of serving the mission of the site, perhaps the "Highest Voted Questions" including some of the more subjective and less 'answering' question is detrimental. It does provide a poor impression of the site.
However, it is an accurate depiction of the community, which is what forms the site. Filtering out questions that are highly voted from the highest voted questions is betraying two people: the visitors who are not seeing what is actually the highest voted posts, and the users who did get those high voted posts not being properly attributed.
Regardless of whether a person thinks a certain question doesn't mesh with the purpose of the website, it does no one any good to obfuscate the hard numeric data on the grounds of soft subjective data. This is akin to taking the top 10 scorers in a school, but deciding to filter out Alice because she is disruptive in class.
If her academic merit places her in the top 10, then as long as she is a part of the school she has a right to be on that list regardless of her behavior. Likewise, as long as a highly voted question remains on the website, it has every right to be counted in a metric for the highest voted questions.