I found who I think is my husband's great grandfather from Lucca, however, this immigration record states that he, along with all the other names listed died at sea during the voyage. I see another name just below his that indicates this man is a friend who sailed with him to immigrate to N.Y., and on to CA., and both came from the same region of Lucca.
My question is: Wouldn't there be another ship manifest record while he was still alive prior to the time he died on ship, and were the corpses buried at sea or sent back to the family of their hometown origin?

Any response without viewing the manifest would be pure conjecture. Can you give the name of the immigrant, ship name, port and arrival date?

People who died at sea were usually buried at sea for the simple reason that there would be nowhere to keep the bodies, to say nothing of the cost of return to a hometown. After all, most emigrants were emigrating because they were very poor and seeking a new life so they would be unlikely to have enough money to pay all the costs of keeping the bodies and getting them back. There should however be a record of him on the ship as a passenger on leaving wherever, unless he was a stowaway - but that would have been recorded on the ship's log.