You should not change their amount. Additional large dockyards might offer additional ships but not as much as the large dockyards that are part of the game when you start a new one. With additional large dockyards you increase the time you need to search for ships, but the amount new ships won’t rise in the same extent.
If this hint is still valid after patch 1.2 has to be verified. The patch increased the number of available ships at large dockyards.
Source: Falko from Patrizierforum