Even if the FTD is not cleared up, both the original owner and the owner of the shorted shares gets to vote. The clearing house just cleans it up via proportionality.
Let's assume 100 true shares out and each is shorted 10 times. Everyone votes and nobody holds paper certs. 600 shares are voted yes, and 400 shares are voted no.
The clearinghouse just reports to the company that 60 voted yes and 40 voted no. Nobody is the wiser... well, except for those who read the fine print.