While the design of a website does not in most cases negatively affect the information it contains, a site's visual appearance can have a major impact on how researchers perceive the site's content. Flashing graphics are distracting. Are there (too many) advertisements? Are the advertisements appropriate to the context of the site? For example, you might accept a few semi-obtrusive advertisements on the homepage of the New York Times but not from the website of a less well-known news outlet. Mismatched advertisements and content are a signal that revenue generation rather than the dissemination of credible information is the goal of the author or sponsoring organization.
On the other hand, a slick, professional-looking site does not automatically confer accuracy, authority, or credible content. Making spurious information look professional and accurate is a common tactic on the open web.