Does it takes longer to cycle a route with a mountain on it comparing to the same distance without a mountain? What is the cause of that?
Say you can keep a 30 kph pace on a flat straightaway. On a hill, that can drop to 10 kph or even less depending on the grade you have to climb. Call it 1/3 of your flat pace. Say that half your run is uphill and the other half downhill, and let's also say that the total run is 30 km.

If you run on the flat at your regular pace, it takes one hour to do that run. But if you do 15 km of the run at 10 kph, you'll spend 1.5 hours just going uphill. There's no way you can make up the time, because you're already over by half an hour. 

Now let's say you go uphill for only 10 km and downhill for 20. You still have only reached the summit when the hour's up.

There's a point at which you can do a short climb and still compensate by speeding downhill, but often you would have to attempt dangerous downhill speeds to make up your lost time. It's just not worth it. What is the obsession with time, anyway? In a race, everyone runs the same course.

Take comfort in the fact that the climbs you do are working your body much harder than running on the flats (or, obviously, downhill).