Take this with a grain of salt, but my understanding is that even without a harbor/customs house, a foreign trade route will be preferred over a domestic one, and will therefore originate if available, so the addition of those buildings shouldnt create new foreign trade routes. What it may do is draw a lucrative FTR away from one of your bigger cities to your smaller H/CH city, which could be detrimental if the bigger city has commerce multipliers that the smaller lacks. Note also that the 100% yield on an FTR is on the base profit, and most of the final FTR value is due to modifiers such as extended peace and its nature as a foreign route (mouseover an FTR in the city screen to see the breakdown). The base profit is, if memory serves, a function of the populations of both cities, and usually around 2 commerce.