Spoiler: (highlight to see... unless your screen is different from mine) My favorite way to handle the zombies in Bonehorde is to sucker them all to the fire arrow trap room... get six or seven following you and they all go down like dominoes
. If you holy water them before they "wake up" they only take one shot... same thing with flash bombs, but flash bombs will wake up others in the area, holy-water arrows won't. And remember the haunts (undead with swords) and undead priests can be killed with a single blow from a short sword if you manage to catch them unaware, backstabbing them.
There are two more missions in the game that are littered with undead, but they are both more manageable than bonehoard.