Each ship hanger has a desired surplus crew count. This value can be changed in the hangar view. When a ship is created from that hangar, it draws upon the pool of excess goons to fill the desired crew count. As the goon pool drains, the ship may not be able to fully staff the desired count.
Having lots of crew on board your ships has many advantages. Crew members can repair damaged hull and armor components. They can also fight off foreign invaders that find their way on board the ship. Alternatively, goons that are not on board your ships can be sold at some space stations for various commodities.
You'll see escape pods being ejected from destroyed ships. Retrieve escape pods to recruit more crew members. Pods of an enemy faction may not accept their new life as a pirate, and will be frequently tossed out the air lock. If the captured crewman accepts pirate life, that ship's crew count will increase (low faction relations and high ship crew count will decrease conversion chance). If a ship ends up with more crew than the desired crew count, the extra crewmen will be deposited into the pool of excess GOONS when the ship warps, refits, or goes back for repairs.