My guides tend to be aimed at country level economics and I guess would not adapt well to what was a city state. However you are correct that it would be more realistic to work out the naval workforce and some sort of replenishment rate. But my guides try and simplify complex processes to make them easier to calculate in a sensible logical manner.
If you worked out the net population growth, you could work out the limit for men that could be lost in a year and I think that is a welcome addition but does complicate matters and does not actually help to much in terms of economics. The reason for this is as follows.
The assumption at the start is that everything at the outset is paid for already, we are merely working out the maintenance of public goods within the realm/country, so we account for regular costs/depreciation/replacement costs averages etc.
You discuss the manpower aspect as important, and yes I to think it is important as mentioned in my guide, it represents the most costly aspect of our navies, in supplies, wages etc.
I believe you could work in some way of representing this within the equation as perhaps an average human replacement cost. This would be the cost to the state of replacing each man with a native or a mercenary. Demographically speaking you could also workout the the proportion of the population that is involved in naval duty much like I did in one of the episodes for the army if you want to work out the manpower size.
Needless to say, I certainly support adding this in, but believe it makes things unecessarily complex for my purposes and the purposes of my guides. I do encourage people to use my work and improce it where possible.
PS: Love Europa Universalis, it probably inspired in some way to making this guide.
PSS: I dont contest that Athens navy was that big however I would contest that a city state keeping a navy that size in running order is rational. Another point I should make is that when you talk abouyt Athens they did not having a standing navy as such, certainly I would contest that Athens would of had 200 standing triemes all the time. I believe at the time that during periods of wars and potential invasions i.e. Salamis that merchant ships were rented, commandeered etc and enlisted into the navy for that period. The guide generally deals with a standing navy because it is very hard to depict a navies cost without it being a standing navy, because costs are dependant on whether there is war or invasions etc. This is an important difference between the example you gave and my guides.
In the same way I would pressume that Athens did not have a standing naval manpower of 40,000 men, but that civilians were supplemented into navies as well as mercenaries and mercenary ships. I make this assertion because I believe the population of Athens would not of even been close to 40,000 at the time, considering Corinth in 4th Century BC population was about 15,000 people. Therefore I would suggest that Athens did not have a standing navy of 40,000 men but rather used this amount to fight specific battles.
My guide is for standing navies and thus manpower is less important, but still an important factor.
Anyway good post, got me thinking...