I've just started my first real game, but even in the test world both options would have been helpful.
Option 1 should definitely be implemented, saves me a lot of time and entries in the route list as soon as you have routes (or route combinations) longer than a day. As a plus, it only needs a very simple UI, just also have a day selector on the schedule route page.
Option 2 would also be nice, but only makes sense if the sub-routes are be default combined in the manage route display. I don't know how the system determines for example that you are flying daily or not, but if the flight number has an influence, options 2 becomes much more useful. Maybe limited that the flights have to started inside x hours. The suggestion of adding A, B, C etc to differentiate is also nice.
Conclusion: I vote for both options, as the tackled problem isn't completely the same.