Holes in my upholstered shell?  

Holes
Are from the factory for injecting foam.

Actually
I think the holes are from the factory to let out air when you sit in the chair. It can escape though the fabric if it is porous like hopsack, but not if it is upholstered in naugahyde and not as fast as it can if there are no holes.

Pegboard
You may be right depending on the age of this particular chair. It looks like it may have had shock mounts originally?
On later padded shells (1971+), the holes were used to inject foam. Also, these shells no longer used shock mounts.
http://eamesdesigns.com/catalog-entry/pac-1-1971/