I understand there might not be an OBVIOUS reason why themes would matter, but there's a lot we don't know about google and I can see reasoning behind this and would hesitate to dismiss it as "stupidity", especially when getting rid of that stuff is good practice anyway.
For one, a few people mentioned that the themes are getting pinged upon, hence update notifications etc. Secondly, someone else mentioned the possible security flaws in certain themes. There are some themes I wouldn't even upload once if I were trying to rank a site, and next time I make an authority site I am definitely going to research the theme I plan to use much deeper. I generally like to use a free theme that has good updates and support (hard to come by yeah). Recently I was building a site and was trying to tweak a theme which is very, very popular. In my research I ended up at the place where the theme creators submit their themes to WP for approval to the marketplace (sorry can't remember the proper name of it). The theme apparently had a large security flaw exploitable at one point and I mean these ppl put the creator thru HELL to fix it. And I mean these people are real assholes, think official adsense forum asshole level except wayyyy more anal. It wouldn't surprise me if themes that have historically had problems somehow find their way into G's algorithm in a negative way.