The main problem with boosting the price of ships is that there's not a commensurate increase in gameplay optimisation. With the current meta, most situations don't actually call for the use of a navy- the extremely generous military access treaties (ie 'most people will agree unless they hate you, and if one person from one alliance gets access then everyone has access') mean that you only really get benefit from ferrying troops across oceans or channels rather than from coast to coast, and since navies have no real effect on your supply lines and there's no blockade CBs that let you take land, there's very few ways to directly leverage navy -> expansion in the same way that you can leverage a building that offers ducats/manpower/cheaper governing costs or that you can leverage a land unit.
This means that navies are almost always an auxiliary unit, designed to provide situational convenience rather than absolute military superiority. Even if you're in a situation where you have absolute naval superiority- such as a player-consolidated Madagascar or Philippines vs Kilwa or Ming respectively- you're usually better off declaring a naval war to take money and using that to invest in an actual army, instead of there being any real way to expand navally.
The prices of ships thus reflect this supporting role in the game's systems. This makes increasing the costs for realism's sake a bad idea, because if something is overpriced for what it gives you, people simply won't use it. You're not going to invest in a level 3 monument or trade centre if there's still high-value workshops to place down, and you're not going to invest in a navy that costs as much as your army when you could be using that to replace infantry with artillery or cavalry and get much more out of it.
