As of SNS HDR-Pro 1.10 there is a batch mode. You load up a directory with the hdr sets (only), tell it how deep the stacks are, then let it go. All the stacks must be the same depth. Unfortunately there are a few issues...it doesn't seem to handle 16 bits tif as an output target, and it takes about 7 minutes to process a 3 deep stack of 21mp tifs. And it doesn't link to Lightroom, but that's just me being a big baby.
But the biggest drawback is that it doesn't (yet) apply the current control panel settings to the stacks it is processing. Rather it applies it's own internal heuristic processing which BTW yields essentially perfectly processed images by default, but perhaps not exactly what you want.
It should be noted that the developing control paradigm on SDS-HDR is one of the best I have ever used for processing photographic images, even ignoring that it is also developing an HDR stack. After playing with the dismal, plodding, ass-backward CS5 HDR-Pro controls I am all the more impressed. Software design by committee, that's the only excuse Adobe can make. Somebody on the committee was very good at eliminating ghosts, but nobody knew what HDR was actually supposed to do, their entire concept of HDR must have come from viewing Flickr fantasmagorias. Please, for CS6 can we have less content-awareness, and more HDR. Thanks.