In real life, there is interest and inflation.
Money you are investing needs to return you more than that or you have no profit at all.
It is the same in civ3. I am not an economist, and i am not planning to calculate or estimate the actual numbers for this in civ3, (which would most likely vary for different era's) maybe someone else would like to do so
There are many ways you can invest your resources, varying from an army to settlers to factories or marketplaces. They pay back in cities, shields or gold.
Your empire grows in a sort of reversed piramid form trough the payback of all these investments.
This should allow you to calculate a common interest rate.
As i said i have not calculated it, but i'm pretty sure courthouses' payback will not reach the common interest rate by a long shot and thus are a waste of resources.
It is similar to doing an investment in real life with, say a 0.5% return on investment per year. Yes, it does give you profit, but it is so small you better invest your resources elsewhere.
Of course this is just an over complicated way to say that it is merely less efficient than building other things.
(which also is the case for your 0.5% profit investment)