Nope, subs are not factored in. I always put in a player in the final few minutes to earn a bonus green. Lately, I've been using reserve players. However, their morale continues to plummet.
However, I discovered that if I don't train the players the max 48% daily, their morale won't drop. So heavy training is a factor.
Edit: The new season will apparently have a morale level added in. Let's see how that works out.