Yes, they are Emplaced Weapons, and accordingly can ONLY be manually fired by a model inside the structure, note this is different to the "gun emplacement" options available to other fortifications.
and if so does that mean the silo is always indirect since you can't see anything over the walls of the battlements?
It will use True Line of Sight like any other weapon, generally you will be correct, although in theory a particularly large model could possibly be visible to it.
Second question when indirect firing if you score a hit does it stay there or does it scatter the little arrow but you subtract your BS skill? The wording for this seems kinda wonky, Pg.34 When firing indirectly the BS skill is not subtracted unless a hit is rolled. Which to me says that you minus BS on a hit. However the picture below shows a hit and it does not move at all.
You are putting the "unless a hit" bit with the wrong part of the sentence, they are saying "unless a hit is rolled on the scatter dice, the blast marker always scatters a full
2d6"
a Hit is still a Hit and acts the same as a Hit under the blast rules does.