I actually thought about the same feature, also regarding the fact that the seperate "trader ships" would be removed, but a little else.
What I think would be nice would be:
Being able stack cannons in your warehouse (that would also make it easier to sell them if you have like 20 of them, as you can only sell them 1 by one atrm)
Make it kinda like you said with the amount of deck guns, so that you can say "Hey, I want only...5 of 14 cannons on my lower and middle deck of my 3rd Rate and like 0 of 9 on the top deck."
While each cannon has a percentage X it reserves as OP mentioned space for needed crew, ammo etc. depending on the ship
and each ship has a maximum and minimum cargo capacity (let's say 10 to 20x the current amount of the war ships when it would have NO cannons mounted and e.g. 10% reserved which would be the value they have now).
I would go with a percentage for guns instead of a fixed value because it would probably totally kill the smaller ships in capacity when it is too huge or make big ships the best traders ever, if it would be too small.
The percentage would adjust with the total amount of guns of the ship so e.g. a 3rd Rate with it's 2 bow, 2 stern and 2x 37 side cannons (14+14+9)and the actual fix cargo value of 350 would the maybe go with
Minimum Cargo Capacity: 350 (all possible cannons are mounted)
Maximum Cargo Capacity: 3500 (wiith the above mentioned 10x more Cargo and not a single cannon mounted)
Cannons: 78 (2 Bow, 2 Stern, 2x9 Top Deck, 2x14 Middle Deck, 2x14 Lower Deck)
in the below linked google-spreadsheet anyone can calculate this the way i meant it. but remember: 100% Cannons = only minimum Cargo
https://docs.google.com/spreadsheets/d/1f5FEpmN-ffkUrdEsLXrf2_7c7v0NolWrIY7KXoFH0zE/edit?usp=sharing