Are there any reasons to go through non-civilian sectors?

In FTL, some sectors are marked "Civilian", some "Hostile", and some "Nebula".

Is there any reason why you might choose a Hostile or Nebula sector instead of a Civilian sector? Will you pick up more scrap from enemy encounters that way? Is that not cancelled out by scrap you might get from beneficial encounters in a civilian nebula?

That all depends on how beefy you are at the point that you choose where you're going. Civilian sector doesn't equal completely safe. A hostile sector, while a bit more unsafe, also generates a bit more reward for being risky. This is in the form of special encounters and shops. Also, as said before, if your ship is decked out and has more shields then most things do, you might be safe enough to trounce anything in a hostile sector, thereby gaining valuable scrap for nothing. Also note that you WILL have to defeat a large opponent at the end of the game, and you will NEED to have your crew leveled up on Helm, Shields, Weapons, and Engines before then. If you avoid every battle, this will never happen. Getting into fights and having them dodge things or charge the weapons is the only way they get exp. If you're having a hard time on a particular run of the game, choose neutral sectors. Otherwise, I would go for the more hostile ones myself.