Yes, if you go to longarm sites, you will see that people do special things to quilt with batiks. The weave is not as "malleable" as other cotton, so when the quilt is quilted, the holes left behind are bigger (but will close upon washing anyway).
I personally have decided that I won't ever do an all-batik quilt because I don't like quilting them much. However, a few pieces of batik in a non-batik quilt is just wonderful.