Are self pollinated plants genetically different?
Yes, it does.
In Meiosis there is genetic recombination (by recombinase) in the Meiosis-1. So even though it is self pollination, there is significant genetic variation.
Still for higher degree of variation cross pollination is exhibited.
It should be noted that cross pollination has greater evolutionary significance.
Few plants exhibit self-incompatibility to supress self pollination (in monoecious flowers/plants).