Actually, if you want to add ships and defenses to the pirate base grav well, you'll have to edit their template in GalaxyScenarioDef.galaxyScenarioDef file:
planetItemsTemplate
templateName "Template:PirateBase"
subTemplates 0
groups 1
group
condition
type "Always"
param ""
owner "Pirate"
colonizeChance 1
items 52
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Heavy"
item "Pirate:Frigate:Scout"
item "Pirate:Frigate:Siege"
item "Pirate:Frigate:Siege"
item "Pirate:Frigate:Siege"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:AntiFighter"
item "Pirate:Frigate:Medium"
item "Pirate:Frigate:Medium"
item "Pirate:Frigate:Medium"
item "Pirate:Frigate:Medium"
item "Pirate:Frigate:Medium"
item "Pirate:Frigate:Medium"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"
item "Pirate:Module:GaussDefense"