I suspect the morale bonuses do work to one level or another. From experience (no scientific testing i'm afraid, didn't realise it was in doubt) when troops are recruited in cities with multiple morale bonuses (temples/special buildings) they seem more enthusiastic on the field. i.e. I often have 'impetuous' troops as compared with 'eager' for troops from other regions. Seem harder to discourage also.
Could just be my imagination and terrain of the battle however