Pretty much what @Jerome said. Privateering / trader raiding is a playstyle and if it didn't exist we wouldn't need people to transport their resources around the OW at all as it would mean nothing but wasting time. Also people could still build ships in capital areas but with lower chance for perfect builds, so I don't see the issue.
People who can't handle losing traders and want a completely safe economy should stay in the greenzones or move their character to the PvE server altogether... and people who are able to put on their big boy pants and take a risk get a higher chance for perfect ships when building in free towns in return. You risk more, you get more reward. Seems logical to me.
Raiding traders should always be a thing in a OW Age of sail mmo game. It's a given in my opinion. Otherwise we can do away with the crafting aswell and let people pay gold for "building" ships directly. Safe traders and economy with no downside at all on the PvP server is nothing but a joke...
Well, can't be more meaningful than at free towns, if the safezones can't be captured, right?
Simple way of fixing this is a only very minor increased chance or no change at all at free towns and a lowered chance everywhere else...
Well, it's the best way to get hotspots for raiding, trade and PvP... if it would change all the time, people would get tired of moving their assets and rebuilding etc. .