Why do accelerometers have holes etched in their masses?
The holes are apparently to control the damping. Damping appears to be passive on most of the accelerometer designs so the flow of the gas through the holes will determine the damping. Damping is important- you don't want the proof mass to bounce around too much. Ideally it should be more-or-less critically damped, I think. 

Without the holes, the mechanism of film fluid flow would be different- and possibly less linear, leading to bad effects such as excessive vibration rectification.