Very basic questions. This is my first 18xx.
1. If a route passes through an unoccupied city, does it score? I'm assuming yes.
2. Can company B's route go through an upgraded city (two city spots) if one of the city spots is unoccupied and the other city spot is occupied by company A's token?
Yes, it can go through (and out another direction) as long as there's even one unoccupied spot. Only if all the spots that are there are occupied must the route stop at that city.