Watch the pattern the reaper takes and the timing of its random turnarounds. Sneak past it like Solid Snake, or shoot it from behind without getting in its line of sight. If I remember, you only get one arrow in the air at once, so if you're close to the minion chain he summons, you can pop all four of them really fast.
The hammers are used in the dungeon maze levels (every fourth level) for freeing the statue guys that help you with each boss.