Yes, the 3 cruise ship piers were damaged but are being repaired as we speak and 2 can already accept ships along side again (1 at a time).
The rest of the ships use tenders, which by most accounts are modern, efficient and not a problem - see this thread for more: http://cruise-chat.com/eve/forums/a/...1/m/5751056912
The piers should be open fully by the endof this year, with the exception of Carnival's Puerta Maya pier which will need until next summer.
You can find news and updates about the piers and the island in general on this Cozumel information
Otherwise the island is in excellent condition!
Hope that helps