The program reads all CFG files, located in its main folder and in the conf.d subfolder, and gets all ships' definitions together. To reduce the number of ships just remove relevant CFG files (you may also change the extension to something other than CFG).
This is what the readme says, by the way:
**** Customatisation ****
The config file aicarriers.cfg is located in the installation dir. Some items can be configured in it, just follow the syntax.
You can also add independant formation files in the conf.d directory. If you modeled a landable ship for FSX, you can provide a config file to be put in this directory.