I used to have a hard tonneau cover but opted to sell it and replace with a camper shell instead because I did not want my dogs riding under there for reasons you mentioned plus it doesn't seem very fair to the dog to not be able to stand up, stretch, etc...
Now I let them ride free in the back with the vents open for short trips and strap their kennels in for longer trips. The plan for hunting this fall is to have the kennels in the back strapped in and all the rest of our gear (decoys, waders, etc...) can fit around the kennels.
The only snag I have seen in this setup is when it gets hot (80* plus) I do not feel comfortable with them riding back there due to lack of circulation so if it's too hot out the pups stay at home.
FWIW - I sold the fiberglass bed cover for $300 and bought the shell for $650 so only spent $350 for the upgrade. I can still lock everything securely in the back, my dogs ride comfortably and the cab of my truck stays clean. Craigslist is an awesome place