Economic models inside this game fascinate me.
Short Version: Salary Per Voyage / Provisions is more economically stable in this situation because it does not penalize any group of players over the other (alt makers, eco-players, pve, or pvpers), it rightfully places the expense of the ship on a per voyage bases, and it doesn't introduce a mechanic that could be exploited by the hardcore to the detriment of the casual.
Long Version:
By using crew as a resource it would be more historically accurate. Certain ports were known for their ability to muster men; this has merit. Nevertheless, as the theory is proposed the resource would be a finite renewable resource with battle / sailing effectiveness consequences.
So before I go into why adding a voyage cost creates the desired affect without the negative consequences, let me ask some questions?
How many crew can be banked in a Barracks?
How many Barracks can a player have?
Does it require an outpost to Barracks crew?
Would players have to consider positioning a barracks in their building slots?
Would players be given their full compliment of crew (based on rank) per day, or would it be smaller?
What would the refresh rate be?
As one sails through the day, based on the answers to these questions, a captain may choose not to participate in a Defense of a Port even though they have a ship in the area and are familiar with port battles / pvp inclined due to their desire to bank or prepare resources for their clan's operations.
One may choose to barracks crew in a non strategic location and be penalized as they try to re-position their barracks. (When the outpost mechanic already has this affect, why introduce another?)
I like some of the concepts shared, e.g. skilled-crew are a renewable resource but base crew are everywhere...
But really the OP makes it sound like this change is driven at realism of cost and not intended to penalize players for playing risky or making strategic decisions that don't pan out because of timing / ganking / placement / resource renewal rate / blah / blah / blah....
So instead of introducing a finite renewable resource, why not make voyages cost money? Mission and PVP rewards would need to be re calibrated, but before leaving port you simply pay a crew fee based on the intended journey. Each time you press the sail button a panel comes up asking you to pick a Voyage type.
For example:
Manifest: Transport - Crew cost 200 gold pieces
Trait: 2% faster open world speeds
Manifest: Trade Route - Crew cost 500 gold pieces
Trait: 5% lower prices on one resource at destination port
Manifest: Combat Route - Crew cost 1500 gold pieces
Trait: 2% improved reload speed
Manifest: Port Battle - Crew cost 50% of Spoils no upfront payment
Trait: 2% increased damage to Siege Targets
With this system you introduce an expense that promotes planning, rewards players, and doesn't penalize those who don't farm up or position resources. It treats casual and hardcore players equally. It's all carrot and no stick, except the costs should GO UP for larger crews on bigger ships. This portion of the mechanic would be control by a query when you press the sail button to determine crew make up (officers / upgrades: hammocks, marines, etc.) and ship type.
Another incentive could be added where if you sail a ship over and over, theoretically keeping the same crew, the cost gradually reduces. Five back to back voyages with a Cutter may reduce your expenses by half, because of engendered loyalty. Or perhaps the first voyage on a new ship requires a premium crew rate in order to staff the ship with the basic crew?
I don't know, but adding a finite renewable resource that ticks on the hour which affects game play effectiveness negatively is a mistake and will drive less hardcore players away.