As for the Enderclams; I don't think it makes sense for them to be found underwater. Ender creatures are hurt by water, after all.
Well the trees can't be grown back, and you don't get much blaze powder from one tree. So I would assume that once you have depleted all of the trees around you would need to start fighting blazes. The mod is more geared towards peaceful players though, so it fulfils its purpose perfectly. It eliminates the need to fight anything.
Not too sure about the enderclam issue though, where else would I put them?
How else would I implement ender pearl alternatives?
They are quite hard to collect too since you need to create a bubble around them under the water since they take ages to break. They aren't the most common either.