Many hand quilters say batiks are hard to needle, but I've never had a problem, with one exception. I wouldn't use Warm and Natural as the batting. I also have no problem appliquéing with batiks.
The only time it was hard to quilt, was when I had to hand quilt with batiks on the top and the backing. I could have used a jackhammer to get the needle through the sandwich.
If you try it, keep the tension a little loose in the hoop.
good luck!
Janet