That sounds pretty normal. Depending on the type of surface you walk on, the cleats will periodically hit the ground.
I've never wore SIDIs before, so I can't comment on your specific shoes. I wore a Northwave MTB shoes. At the beginning the cleats never touch the ground, after about a year the sole wore off enough that the cleats will contact the ground.
Having cleats too recessed can also be bad, you'll have a hard time clipping in. Some shoe manufacturer will actually recommend cutting the threads down if you have problem clipping in.