It does seem strange that there are no permanent quarters for the guards or a dedicated mess hall for them.
But personally, I think it's a trivial concern compared to some of the other things that I am sure the developers are working on, like fixing the attribute system, balancing combat, and making the rest of the campaign look and play as beautifully as Fort Joy. Tinkering with the prices of fruit and paintings while in the first Act is pretty low on the list for me.
Also, I found the economy in Fort Joy brutal, as I think many did. And I liked it. I liked that you couldn't just steal everything and make tons of money and buy all the skills. When I finally did save enough money for one of the expensive skills, I cherished it even more. Just my two cents!