Right. There's not actually much 'biomonitoring of brain activity' that is currently possible. You can put electrodes around your head to measure the tiny electric fields generated by all the sub-microscopic ion streams squirting around neurons, but the spatial resolution is pathetic, and you can only really see the outer surface of the brain. You can do functional magnetic resonance imaging to monitor blood flow in 3D with millimeter spatial resolution, but how blood flow relates to neural function, let alone mental function, is unclear. That's about it, as far as I know. Oh, yeah, there's positron emission tomography, but that's just another way to measure blood flow.
It seems unlikely that auditing would have any particular effect on these crude measurements, anyway. All the input is in fairly sophisticated words, right? That means that if it's affecting the brain, it's doing it at a pretty intricate level. Trying to detect effects of auditing with electrodes or fMRI would be kind of like trying to compare the effects of different strategies in Halo by watching a magnetic compass sitting on top of the XBox. It'll swing around a bit, maybe, but not in a way that tells you much about how things are working out for Master Chief.
Of course, if fMRI and PET and electroencephalographs are too crude to tell us much about the mind, the implications for the e-meter are pretty dire.