Well, uhm.. morale seems to affect how the players play in a bad way, yes, like I have noticed if a player has poor(ish) morale, they are more likely to get a card, and/or a lower rating.

Fitness is a category in the skills third column, I think it affects how likely they are to get injured. I think this 'cos my guys rarely get injured.

Condition, the one you can fix with greenies, I think also seems to affect the rating of a player in a match, how much they get out of training, and also how likely they are to get injured.

This is my opinion from observing my teams. Your results may vary from mine.