Extended cruises will indeed slow your game down, especially reloads of saved games. I wouldn't worry about that too much though. It's just a minor annoyance.
Here's the big problem. Remember that the only time you can receive upgrades to equipment is after you end a cruise and the blind chimpanze tosses his dart at the board. The longer your cruises are, the fewer times you come back to port. The fewer times you get back to port, the fewer upgrades you receive.
Extended cruises are a great way to be skippering an oudated Tambor in 1945! That is if you live that long. Accumulated hull damage has a nasty habit of becoming fatal at the worst moments...
