WTF are they feeding those chickens, and can you use the eggs as flash-bang grenades?

Seriously, the game designers are seriously deluding you. It was not only not common, it didn't happen at all.

Manure is not explosive. This is really a topic for /r/askscience on "How do so-called manure explosions happen?"

It's not the manure exploding. It's the modern handling of manure on huge pigfarms and such that results in a secondary product exploding.

To have a "manure explosion" you need to have large amounts of feces, huge amounts of it. Then you have to put it in dugout manure pits, and cap it so no odor can escape. This also means that the methane produced by the decomposition of the poop can't escape and builds up. You know methane. It's the fart gas that some people set on fire. Once you have enough methane, it only takes a spark to set it off. Talk about an Expedient Incendiary Device!

These did not occur before very recently. They certainly would not be discovered in cultures like the medieval European where feces of all kinds were piled in heaps on the surface of the ground, then spread on gardens and fields. The methane is diluted and blown away as soon as it is created. So it actually stinks less.

Consider the essential silliness of the method described. First, the assassins have to tear up the floorboards or tear down the ceilings. Then they have to sneak in several large wagonloads of fresh poop and distribute it around. Then they have to see that the floors and ceilings involved are absolutely air tight so the methane won't leach off. Then they have to figure how to keep the residents from smelling it, just from them hauling it through. Finally they have to keep it from being set off by a spark from the fireplaces or a hot chimney when the person they want to kill isn't there.