Pros:
Tentapillars connect to Tentacles in Overworld, if the Tentacles are a pain to kill (grouped) kill the Tentapillars one at a time. - Perhaps Tentacles could regrow unless the Pillar was killed.
Holes in the ground allow for co-operation between shards with players.
Potential for bosses to actually be in the ground, half caves, half overworld.
Plan massive attacks by leading the boss to a hole and then throwing down a bunch of bombs 
Easier to determine which cave entrance goes where.
Cons:
Extra stress on the Server Host
Holes can block the way, or even create a dead end.
Grouped up tentapillars can cause issues and prevent moving through the caves.
Probably some more.
What would you add to this list, and would you like or dislike it?