Can you describe more what you're looking for ?
A hole on both sides (i.e. you're right above it) will just give you an extended water column on the SI display.
If its on one side only you'll most liekly see a shaddow as you expect if you're looking for an hole.
Really comes up to the size and deepth of the hole and your distance to it.
Or what kind of holes are we talking about ?
/del