All the certs involved for the client's app should be the client's certs. You should even create a separate developer's cert for yourself under the client's account.
These certs not only identify the distributed apps to the technology of the App store but are also the apps financial and legal IDs. In other words, the certs control who gets paid and who gets sued.
Neither you or your clients want the other's certs entangled with their own. If you do entangle the certs, your client might find they can't administer or update their own app and you might find yourself responsible for some future action of the client.
You might even want to go so far as to create a separate user account on your development Mac for each client in order to keep all the certs and profiles cleanly separated. It's a pain but these certs and profiles are the very heart of the App Store system. If the certs and profiles get scrambled it's a big, big deal. As in money, guns and lawyers big deal.