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Some ships that spawn will drain resources from a shipyard but not all. Ships built at a shipyard will have a job to do. Military ships will patrol and can help a faction turn the tide of battle. Ships you self sell to a faction shipyard will also be used by that faction. Trade ships will trade and miners will mine. The shipyard will still produce ships at the same pace as it does in vanilla.
With all that being said, a war of attrition is possible but it is done by controlling zones rather than destroying an economy. Of course stopping a shipyard from producing ships will also help your war cause but it isn't a huge impact since most fleets are spawned by zone ownership. This could be changed, we have the code in place and capability to flesh this system out in a more complex fashion but that is not a goal at this time.
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