A lot of cotton batts are needlepunched through scrim now. Makes the cotton much more stable, can quilt lines further apart, etc. Scrim can make handquilting more difficult, but is fine for machine quilting. In general, you want the scrim side touching the backing of the quilt so when you machine quilt, the needle is punching the batting in the same direction as in the factory. (That's if you can tell which side has the scrim. Warm and Natural describes how to tell which side theirs is, but I don't know about other manufacturers.)
Incidentally, not all batts that are needlepunched are needlepunched through scrim. Quilter's Dream cotton is needlepunched but does not have a scrim.
There is no reason to prewash a batting that has scrim.