I noticed that there were only one or two corpses there after killing the boss on my last playthrough. The only thing I had done different this time, was that I skipped past most of the enemies in the level (took both shortcuts). So I backtracked and killed everyone (without going by the nexus), even sniped the two above the Istarelle ladder location, and went back to the boss area. Now all the loot was back; a giant club, crescent grasses, 2 shards and 1 chunk of faintstone.
So I guess that some of the enemies you kill 'fall down' into the boss area, leaving additional loot there.
I replayed the level on the next game cycle: Killed all enemies, especially all 'sleeping' and hiding enemies, even picked up the Istarelle (was pwwt). After beating Leechmonger there were 2 shards of faint, 1 chunk of faint, a giant club, and a bunch of crescent grass. I believe the shards of suckerstone are there regardless.
Replayed the level on another playthrough. Killed all enemies, but this time a lot of the loot was missing in the boss area, so I went backwards through the level and pushed a lot of the corpses into the abyss. When I walked back down to the boss area all the missing loot had appeared there.
A note on the 5-1 Crystal Lizard:
After killing all the enemies (not istarelle trolls) before killing Leechmonger and picking up the loot there, the Crystal Lizard in 5-1 would not respawn when I went backwards from the 5-2 archstone or reloaded profile (this was also after beating Astraea, looting the other Lizards, and doing the Selen sidequest). So I had to start at the 5-1 archstone to make it respawn, strange.
Another approach, by iGBx at the forums:
When you kill 5-1 boss, theres a few items scattered around the area. Go to Nexus. Spawn at 5-2 Archstone and double back to 5-1 boss area and there will be a few more items to pick up. Kill 5-2 boss. Go to Nexus. Spawn at 5-2 Archstone and again go back to 5-1 boss area and theres more treasure. Kill 5-3 boss. Go to Nexus, and again back to 5-1 boss area for more treasure again, including Shard & Chunk of Faintstone & a Great Club.