Pangaea answered me this same very question just a while ago so here it is:
Not sure about the exact formula either, except that Harbours often make little sense to build. It's actually not +50% of the final you see. It's a +50% multiplier on top of the others. And you get multipliers for connection to capital, staying at peace with other AIs, the size of the city, etc. The +50% isn't on top of the final output, but in addition to these others. This means that often you get no boost at all (in the beginning with few and poor trade routes), so the building does nothing, or you get +1-3 . Not a lot.
The benefit, if you can call it that with such a relatively poor building, is that you get the boost to rather than, so you get the multipliers on top, but that is only if you actually get extra from the building to begin with. I usually don't build harbours or customs houses, but they can be good in big coastal cities, and of course there is the added health too.
If you install BUG [or BUFFY for civ4 vanilla] and hover over the building icon then you will see exactly how much every building adds. Very, very useful, so I highly recommend you try it out. There are many other benefits too, as basically every screen in the game offers more information than the default game.
Here is a picture from a size 21 city in the end game, that doesn't have a harbour.
Not a great deal as you can see. The +50% will get added on top of the others you see in the above screenshot, and the Dakyanus trade route already have +180%, so another 50% won't do a great deal.
I think the +50% works on each individual trade route bytheway, so in this example you would probably get +1 per trade route.
). In vanilla, combat is the way to go for most circumstances.
