Researchers look at their papers and for a given conference, either feel they have a very good chance of acceptance, a possibility of acceptance or a long shot of acceptance and tend to submit only if their paper falls in one of the first two categories.
In non-theory areas like artificial intelligence, the committee must take a subjective look at the papers which means many more papers fall into the second "possibility of acceptance" category. Many more people therefore take the risk and submit their paper because they can't immediately put the paper in that third "long-shot" category. This leads to more submissions and a low acceptance rate.
For theory we do a much better job putting our papers into these categories, as we can self-judge the hardness of the results and have a good feeling of the importance of the results for the conference. Theorists can tell when their papers won't have much of a chance of acceptance and will, usually, not waste their and the program committee's time in submitting these papers to the conference. This leads to a relatively higher acceptance rate in theory conferences.
A similar analysis would also explain why the funding rates for the theory NSF program also tends higher than the funding rates at many other programs in CISE.