No problem at all, I do it all the time. I use a range of 16oz and 12oz mason jars (pasta jars recycled) and baby food jars. These I fill to different amounts for the standard steps that I use in propagating yeast from a slant.
The theory behind canning is that you heat the contents to above the sterilization temp of 250deg F. Mold spores and other such nasties can survive regular boiling and sanitization routines, although the actual living organism die. at 250deg F nothing lives. Make sure you pressure cooker goes to 15psi this is need to reach the 250 deg mark.
Someone I was talking to on here said it was particularly useful for high Ph foods as the mold spores could not handle the acid. Hence beer does not grow mold but wort can as its Ph is slightly higher.
So back to the head space (air) inside the canned wort, it is sterilized just like the rest of the contents. I have some agar that I pressure cooked in two baby food jars that I have kept as a control on my last batch of slants. They are still clear despite being 6 months old and the jar only has a tinny layer of wort+agar on the bottom.
Hope this helps, I'm addicted to my yeast farm. I pressure cook my wort which I save from the mash tun, dead space of the boil kettle etc etc. So my yeast is basically free. At worst I mash some two row and get gallons of starter wort to can and save for my next batch few batches of yeast. Having totally sterile wort on hand makes starter prep really quick and painless. I also use my pressure cooker as an autoclave all the time.