I see several reasons:
* Programming a firmware which uses two or more CPUs needs a lot of development to parallelize "jobs" on different CPUs
* PC board layout and thermal management has to be codeveloped/improved
* If there is a need for a 2nd CPU the hardware is more powerful (120point AF system, 40 MPix sensor) and this will increase the system cost.
A specialized camera will see a lower count of bodies produced so the development cost will be higher on a per-body-perspective.
You do realize the current 7D Mark I already uses dual DIGIC 4 chips, right? It never cost $2000, let alone $3000. Making use of dual processors in a 7D II would be a no brainer, and would NOT require the creation of DIGIC 6. The 1D X already uses dual DIGIC 5+ chips, and repurposing that design in a cheaper body would be a hell of a lot cheaper for Canon than designing something completely new from scratch. It also proves that the firmware ALREADY supports parallel processing, so there really isn't any extra work there, either.
You are essentially right. There exist four (?) models which use 2 CPUs and the EOS 1D X which uses 3 DIGICs - some basic development will be there. But never underestimate adaption of existing code for new CPUs with new (totally new?) additional components. And it depends on how you use the CPUs: Sharing load for different tasks is easy, but parallelizing one task is hard to do (except it is sth. like calculating noise reduction for different regions of the sensor).
My third point was perhaps the most important: If there is a need for a 2nd high power CPU the hardware will drive cost - extraordinary fps, a very advanced AF chip, etc. So the additional CPU will only add 100 or 200 EUR/USD but the things that made it necessary are really expensive (high speed mirror mechanism, shutter system, complex and specialized AF chip, ultra fast FADCs, etc,).