The flagship does not benefit from the Dock upgrades, like the other ships available to the Knights, however, it is easily capable of destroying pirate vessels and Ottoman Galleys. If properly utilized and repaired it will be the only warship you require during The Ottoman Fort (on any difficulty), and during Pirates! on the easy and normal difficulties.
"Morgan's flagship is the veteran of a number of voyages throughout the Mediterranean Sea. The Knights of St. John, from their island stronghold of Malta, prowled the seas in long, sleek galleys searching out any who would oppose them, with a special preference for the Ottomans. They had a massive flagship, called the Sant'Anna, but it was so ungainly and expensive to maintain that it was broken up. The masts of Morgan's ship were salvaged from the Sant'Anna; the Sant'Michel has more than a little of her predecessor's wallowing unwieldiness."