A smoke generator has been installed on the left wing of the Boeing NB-52B Stratofortress mothership to assist in tracking the airplane.
Its use during the test of X-38 is detailed here:
Outside I could see the white trail from the smoke generator in the number-2 engine nacelle of the NB-52B approaching from the east
... I aimed my telephoto nearly directly up at the tip of the smoke trail.
As the same aircraft was used during the X-43 tests, it certainly served the same purpose.
My guess, and it is only a guess, is that they are using a smoke generator to make the B-52 aircraft easier to visualize. Typically for flight tests like this they would be doing optical tracking from the ground (essentially a telescope) and this would make it easier to locate the target. (I was going to add also for the pilot of the dropped aircraft, but the X-43 is unmanned)