[Suicide Junkie]

I would expect it to be best for the bigger player to just keep gifting replacement ships to the smaller player.

If you give your little friend all the ships you are producing, he would not have to worry about not being able to produce more on his own due to the limit...
After a while, you could have a combined force of 1000's of ships.

Personally, I see no reason why you should be limited to 100 ships unless your economy simply can't afford to support that many.
However, in a game that was started with the limit set low, the players have obviously agreed on that before hand and the limit should be enforced.