Does a Pokemon's Affection level in Pokemon-Amie decrease over time?
It doesn't as far as I know. I've been raising the affection level of some of my Pokemon since I started and have left some unattended; the affection level did not decrease over the ~70 hours of play time.
There's this site/blog which says (emphasis mine):
Do this five times and your Pokemon will have full Affection, meaning it will be more likely to avoid enemy attacks and will have more chance of landing Critical Hits in battle. This Affection will not decrease over time, so you needn't worry about maintaining it.
And quite a lot of forums on the internet saying the same thing, and I think you can find them easily without my help now!