The mod developers use `Natural Curiousity` Tech to give Scientific and Commercial civs access to specialist workers (in the city screen) that produce 2 beakers and 2 coins as an advantage during the ancient era. You are correct in that building the Great Library (and also Encyclopedia in a later age) will give you NC, since invariably at least 2 civs have it.
As far as I know, they have decided that leaving NC in was preferable to taking it out (it strengthens scientific and commercial civs in the ancient period), since Civ3 engine does not permit mod developpers to STOP GL-like WoWs from giving tech to owners if 2 other civs have it. So, in short, consider it a reward for building either GL or the Encyclopedia.
Hope that that helps.
