One way to do it is to remove them from each and every player entity file.
Example: This is the stock game look here.......
frigateInfo
Page:0
count 7
entityDefName "FrigateTechScout"
entityDefName "FrigateTechLight"
entityDefName "FrigateTechLongRange"
entityDefName "FrigateTechSiege"
entityDefName "FrigateTechAntiFighter"
entityDefName "FrigateTechColony"
entityDefName "CorvetteTechRebel"
Page:1
count 7 <-------------(make sure this number is right)
entityDefName "FrigateTechCarrier"
entityDefName "FrigateTechUtility1"
entityDefName "FrigateTechUtility0"
entityDefName "FrigateTechHeavy"
entityDefName "FrigateTechStarbaseConstructor"
entityDefName "FrigateTechAntiModule"
entityDefName "FrigateTechEnvoy"
NotOnPage
count 3
entityDefName "FrigateTechModuleConstructor"
entityDefName "FrigateTechTradeShip"
entityDefName "FrigateTechRefineryShip"
Change it to this.........
frigateInfo
Page:0
count 0
Page:1
count 0
NotOnPage
count 3
entityDefName "FrigateTechModuleConstructor"
entityDefName "FrigateTechTradeShip"
entityDefName "FrigateTechRefineryShip"
You won't be able to build a frigate with this change I am showing you. However many frigates you do leave just make sure the "count" is correct.