I personally LOVE morale rules.
Games that continue on to the last ship always seem to drag on and on and on. I also agree with previous statements that it is very un-historical.
One game that has great morale rules is Battleground by Your Move Games. Each unit has three "zones" of damage. Green, Yellow and Red. The unit has to make a roll when the damage it takes crosses into a new zone, it also has to make a morale check if in combat in the red.
The chances it will run of course increase with each zone. Units in the Red zone are close to death and highly likely to run.
The zones are different for each unit, some units are more likely to fight to the death than other units. Units also have different levels of morale which is rolled on 2-d6. Units that fail morale turn and run, but may make a morale checks to heal/repair until they are off the table on the friendly side, then they are gone for good.
Morale Rules allow for games to play out much faster. Yes, it is annoying when 2 hours of gaming hangs on a morale roll...and you lose the die roll. But really is that any different than 2 hours of gaming hanging on a lucky critical hit?
Morale rules ought to be really quick and fast. Morale for each ship, and when the fleet is down to 50% (pick a reasonable %) loses, morale for the entire fleet.