Brogan will be able to tell us where it is (and darn it, I'm writing it down!).
Seriously, I have a notebook dedicated just to XenForo, lol. My memory is very bad, so I have to ask questions and write the answers down so as not to look stupid asking them again.
Maybe I'm missing something but my Xenforo doesn't have: Style Properties -> Header and Navigation -> Settings: Height of Header Logo The closest I have is Appearance > Style properties > Header & navigation > and there are no settings for the header height.