Perhaps remove Disguise as a requirement for Advanced Smuggling - it's not really involved in smuggling as it's a bonus to avoid false flag detection, and false flag has little to do with smuggling.
Club Hauling could indeed go to the first mate. It requires some level of synchronisation between the person at the wheel and the person at the anchor, so it's reasonable for the first mate to do the synchronising. Perhaps allow the first mate Maneuverability and Speed Increase so that he can get Club Hauling, though the navigator needs them as well as part of the progression towards Sea Wolf.
Basic damage control as a prerequisite for Emergency Repair seems reasonable, as Emergency Repair is effectively a form of damage control. But I'm less convinced about requiring Improved Potions for Advanced First Aid. If there's a third level Professional First Aid, comparable to the current Professional Ship Defence, then perhaps make Improved Potions a requirement for that.