Do academics look down on well-designed academic websites?
As has been stated several times, there is no such thing as a site being "too well designed."  Of course the design should take into account the audience that will be viewing the site—i.e. if you are designing a website gallery for minimalist paintings, it would be very odd indeed to use as many buttons and links as Amazon.com, whereas for an online store that isn't a bad design at all.

However, in my view, the keynote is really not so much design as implementation.

There are two crucial factors: file size (also known as website obesity), and overuse of scripts (which is closely related).

The website you linked in the comments doesn't load at all in my browser, because I have scripts disabled by default.  I enable them for sites that I expect to run scripts, such as gmail or youtube.

I grant that I may be in a minority of the general web browsing population...but I expect a disproportionate number of academics are aware of such things, and are more likely to be irritated by websites which require plug-ins, scripts and high bandwidth simply to display a bunch of text.

Do your design as well as you please, but try to keep it as minimal as possible on bandwidth, plug-ins and scripts.



(Note: My own personal settings aren't the main topic of this answer, but as several people have made noises of shock at my default blockage of scripts, I'll clarify: I don't block first party scripts that are served by the actual website I'm visiting.)