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.