At the outset, I want to clarify that I am not advocating making salaries larger in general (we all can of course easily do that or not with the options). Any changes that would come from this discussion could be coupled with other changes to base rates to preserve balance. In other words, this is not about trying to increase difficulty. 
I think it is worth talking about two aspects of salary calculations that seem less than ideal.
1) First, the player is currently modeled as a miser, who intends to greedily exploit and abuse his crew by repeatedly cutting their pay even as he himself becomes more successful and wealthy.
By which I mean, the Iron Will perk and leadership skill cause a drastic reduction in crew/officer salary. Crew hire cost in taverns is 1/2 their monthly pay for a month with an average number of days (monthly pay differs by days in that calendar month), so easy to test out the effects, and we also have the formula from characterutilite.c: float leadership_factor = 1.0 - makefloat(leadership)*makefloat(1 + iron_will)/40.0;
So for example, going from level 5 leadership Captain to level 10 leadership + iron will perk Captain cuts salaries to 57% of what they used to be, for both officers and crew. Meaning that in a natural amount of progression from early to mid/late game, the player will start paying his crew and officers only a little more than half as much as earlier.
Personally, I would rather not have my character give his loyal men a 43% pay cut after they made him successful and wealthy.
From a gameplay perspective, I also don't think the late game, when money seems to become more plentiful, is the time to give the player a salary deduction--better to smooth it out and give lower than current salaries in the early game and let them be a little higher in the late game.
Perhaps we should consider Iron will and leadership slightly increasing in morale effects, and base pay being reduced from the beginning, and eliminating this particular influence on salary?
2) Officers are paid very high multiples of a crewman's salary.
Currently, an officer of the low 20s in level makes well over 20 times as much as a normal sailor. Even a low level officer will still be making around 10 times as much.
Granted, it is only a very rough guide, but for comparison here are some salaries from the royal navy during some snapshots of the napoleonic period: Pay in Britain's Royal Navy : Napoleonic Wars : Napoleon Bonaparte :
For the 1793 pay rates, surgeon would only make around 5 times the wage of an ordinary sailor, and a boson would only make about 3 times. In 1806 surgeons are being paid at a higher multiple, but other officers show a similar trend, carpenter at about 3 1/2 times the pay of a sailor, etc.
Now, I'm not sure about privateer pay, but to use the article examples we have as a rough guide to what salary multiples might have been Articles of Agreement Between Captains of Privateers and Their Crews We see that the officers are generally making no more than 3-6 times as much as the landmen, and 2-4 times as much as the able seamen.
From a gameplay perspective, I also think shifting some salary from officers to crew would make sense. In particular, it might make the vessels that can be manned with a smaller crew a bit more attractive (right now, crew salaries are so low I'm not sure that would ever be a consideration, when for a merchant it should be something to consider as affecting their profits). Meanwhile, lower salaries for officers might allow the player to retain some interesting companions they might otherwise feel financial pressure to get rid of.
EDIT: Adding files:
EDIT 2 added comments to files

I think it is worth talking about two aspects of salary calculations that seem less than ideal.
1) First, the player is currently modeled as a miser, who intends to greedily exploit and abuse his crew by repeatedly cutting their pay even as he himself becomes more successful and wealthy.
By which I mean, the Iron Will perk and leadership skill cause a drastic reduction in crew/officer salary. Crew hire cost in taverns is 1/2 their monthly pay for a month with an average number of days (monthly pay differs by days in that calendar month), so easy to test out the effects, and we also have the formula from characterutilite.c: float leadership_factor = 1.0 - makefloat(leadership)*makefloat(1 + iron_will)/40.0;
So for example, going from level 5 leadership Captain to level 10 leadership + iron will perk Captain cuts salaries to 57% of what they used to be, for both officers and crew. Meaning that in a natural amount of progression from early to mid/late game, the player will start paying his crew and officers only a little more than half as much as earlier.
Personally, I would rather not have my character give his loyal men a 43% pay cut after they made him successful and wealthy.
From a gameplay perspective, I also don't think the late game, when money seems to become more plentiful, is the time to give the player a salary deduction--better to smooth it out and give lower than current salaries in the early game and let them be a little higher in the late game.
Perhaps we should consider Iron will and leadership slightly increasing in morale effects, and base pay being reduced from the beginning, and eliminating this particular influence on salary?
2) Officers are paid very high multiples of a crewman's salary.
Currently, an officer of the low 20s in level makes well over 20 times as much as a normal sailor. Even a low level officer will still be making around 10 times as much.
Granted, it is only a very rough guide, but for comparison here are some salaries from the royal navy during some snapshots of the napoleonic period: Pay in Britain's Royal Navy : Napoleonic Wars : Napoleon Bonaparte :
For the 1793 pay rates, surgeon would only make around 5 times the wage of an ordinary sailor, and a boson would only make about 3 times. In 1806 surgeons are being paid at a higher multiple, but other officers show a similar trend, carpenter at about 3 1/2 times the pay of a sailor, etc.
Now, I'm not sure about privateer pay, but to use the article examples we have as a rough guide to what salary multiples might have been Articles of Agreement Between Captains of Privateers and Their Crews We see that the officers are generally making no more than 3-6 times as much as the landmen, and 2-4 times as much as the able seamen.
From a gameplay perspective, I also think shifting some salary from officers to crew would make sense. In particular, it might make the vessels that can be manned with a smaller crew a bit more attractive (right now, crew salaries are so low I'm not sure that would ever be a consideration, when for a merchant it should be something to consider as affecting their profits). Meanwhile, lower salaries for officers might allow the player to retain some interesting companions they might otherwise feel financial pressure to get rid of.
EDIT: Adding files:
EDIT 2 added comments to files
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