Do Zombicide: Black Plague quests last a lot longer than suggested?
We too played the first couple of quests in Zombicide: Black Plague and it took us about 2 hours for quests 2 and 3 and we have played previous Zombicide games.
The first quest we played with 2 people (each controlling 2 survivors) and it took us about an hour and a half, but that included a lot of rules checking (there are huge differences in the rules between earlier Zombicide games and Zombicide: Black Plague).

Game designers give these estimates based on play tester feedback. Play testers may have played through a number of different versions of the same map, be more focussed on continuous gameplay than a group of players and have more experience with the rules and various skills. 

I would treat the given times as "minimum" and probably add an hour to an hour and a half to these estimates.

The upside to these estimates is that if you want to convince your friends to play one more game before they have to go, you tell them "it'll only take an hour, see here it says so in the quest description."