I don't see what being a geek or uber-geek has to do with it. "Honey" is just a form of affection for people in relationships, so why wouldn't Reed (or anyone, regardless of the age and level of geekiness) use it?
I grew up with and have known (and met in graduate school) a LOT of uber geeks.
Not one of them ever referred to his partner/lover as "honey" in my presence.
To this reader, uber-geek Reed calling Sue 'honey' sounded completely artificial and took me out of the story.
