As an interplanetary organization, Starfleet is bound to have encountered a vast variety of cultures and religions. Take earth for instance. It's only one planet and there is however many cultures and belief systems. Now multiply that by x where x is some arbitrary value between 1 and infinity, because the setting has an infinite universe setup.
Now, Starfleet promotes interplanetary harmony among its members. Consequently, that requires a commitment to understanding and equality. Therefore, upholding a strict enforcement to regulate a specific way of life among its officers is rather counter intuitive and grounds by which to provoke disharmony. By contradiction, this can not be the case.
To conclude, I think that the absence of belief systems on the ships in the actual show are more due to producer choices than as a result of continuity. Wouldn't be out of place for there to be some regulations that cause some belief systems to be disallowed while on duty, but this would be due to practicality, not an enforcement.
The actual quote may just be 'wikipedia magic' misinterpreting or misquoting. Or the producer providing it by some choice based on external factors, not necessarily continuity.
And Bob is awesome. QED.
