I'm an adventure photographer and never leave home without 1 or 2 dSLR cameras; sometimes HD video. Though I too will carry my cameras in the trunk section, I wouldn't worry too much about your cameras however you choose to carry them. My Pentax cameras have survived thousands of backpacking mile in really bag conditions. I am amazed at how sturdy they have been.
I was just thinking the trunk vs a pannier the reason being is you could hit the pannier on something doing damage to the camera or if you dumped the bike on the side having the same issue. I am surprised nobody has made a bike specific camera bag... or maybe they have and I just havent found it yet...