@Der:
The Flagship is just a fun unit which represents the “pride of your navy” - a battleship which has the highest morale, best armor and is harder to sink.
As a light-hearted comment, I have to say that if I was a sailor serving on a battleship with the best armor in the fleet and which is harder to sink than other vessels, this would certainly be a boost to my morale. :) Though in fairness, the sailors of the Japanese superbattleships Yamato and Musashi, which served in turn as IJN fleet flagships, started getting restless over the years as their floating fortresses spent much of their their time sitting at anchor at Truk, waiting for Tokyo to commit them to battle. (Part of the reason for Tokyo’s hesitance was that the two ships devoured prodigious quantities of fuel that Japan could ill-afford to waste, and part of the reason was that they were considered to be strategic weapons that were being held in reserve for a decisive battle.)
Over on the U.S. Navy side, by the way, two of the biggest contributors to battleship crew morale during extended missions in the Pacific during WWII were: mail from home and new movies. Both were eagerly awaited whenever supply ships rendezvoused with a naval task force. On the consumables side, ice cream and lemon pie were particularly appreciated by U.S. sailors in WWII (and probably still today). I think there was a tradition at the time which basically allowed battleship sailors to over-indulge on ice cream every Sunday. On one particular such occasion, on the Missouri as I recall, a young bluejacket tried to jump the queue waiting outside the ship’s ice-cream dispensary, then saw to his consternation that one of the people ahead of whom he had cut was Admiral Halsey. (Halsey, who was famous for his hell-for-leather personality but who was also known as a “sailor’s admiral”, quietly told the young man to “get back in line, son.”) Beer was also appreciated, but it was tricky to handle because drinking aboard ship was (and is) prohibited in the USN. US battleships in WWII were sometimes allocated a supply of beer for consumption “off the ship”, which in principle meant “when the ship is at anchor close to a beach somewhere” but which was a problem when the ship was out at sea for weeks or months at a time. Understanding captains would skirt around the regulations by taking advantage of operational lulls when the ship wasn’t actually steaming anywhere: they’d allow their sailors to borrow the ship’s boats, in rotating batches of however many men could fit into them, and load them up with a ration of two beers per man; the sailors would row off until they were a few hundred yards from the ship, drink their allocation of brew, then row back to the ship and let the next group of their buddies take their turn. This practice was probably considered to be a fine example of good old-fashioned American can-do wartime ingenuity.