Faith for the most part isn't generated by number of cities. The amount generated by extra shrines and temples is rather small compared to the amount you'll get from pantheon beliefs which may or may not favor tall or wide - but that's down to the player's choice to choose those beliefs. Science though - even without the science per culture, you will still generate more science total with more cities than fewer. Let's say you have the chance to put down a near-worthless city (and there's nowhere else left to settle). Without that penalty, there is no reason NOT to build that city, since even if it will never generate more than 2 science, that's two science you didn't have before (plus whatever it may earn in other yields). Basically, there needs to be some reason not to spam cities everywhere. They do indeed provide decimal amounts - in the library's case, +0.25 per citizen.