I was wondering if there is a way to use CHDK to control two cameras at the same time in order to take photos for stereo processing.
It depends what you mean by 'the same time'.
You can just press both shutter buttons simultaneously.
For better synch use CHDK or SDM with a USB remote switch.
HOWEVER, use of cameras introduced in 2011 and later is generally not recommended as they are likely to have poor synch unless proved otherwise.
David