It's my impression that it doesn't matter whether a trade route is opened--if it's going to disappear it does, whether you've opened it or not. If it then becomes available again and you want to open it, you have to pay whether or not it has been opened before.
If you have the North American version of Pharaoh, v1.2 is available, which corrects a problem introduced by v1.1 (which corrected a few other problems and added some new things, principally the map editor). If you have the time to download it, I recommend it.