Ian,
Each churchbook is different, but -- if I may comment on what Petra said -- the illegitimate births I see are usually so designated by two features: (1) the baptism is recorded in wavy lines, or upside-down, or sideways, and (2) the "mater" is listed before the "pater", which is not the standard format. Therefore, I wonder if the "C" you have observed is really a flourish above the lower-case letter "u" to show that is a letter "u" without an umlaut?
As with penmanship in the English language, some choose to be a bit more flamboyant! You only indicated that this "C" appeared over names in the register, so this may be completely off-base, but the question of penmanship was truly the first thought that came to mind, so I thought it might be worthy of mention. If one of us doesn't provide the correct answer, you might consider sending to the list a link to a graphic image of a sample entry.
Good luck with your research! With best wishes from Kansas City, USA,
Gordon Seyffert