I've worked with batiks and have done nothing different with them. I don't prewash them, but I do test suspicious fabrics by dropping a piece in a glass of water to see if it bleeds. If you are using a background fabric, it's a good idea to drop that in after awhile to make sure that it doesn't get stained (different fabrics pick up bleeds differently).
Batiks use a slightly different weave than other fabrics. This sometimes creates a problem for long-armers when batik is used for the backing fabric, although that may also be related to the specific machine and batting. You can still mix batik fabrics with other cotton fabrics in a quilt top.
I always do the first washing of a finished quilt in Synthrapol to make sure that any minor bleeds are rinsed away in water. This is true of quilts with and without batiks in them!