In older versions of 7D2D (earlier October of last year) zombies couldn't attack/dig vertically down, and or break ground hatches even if they were present at the surface. The only way they should be able to "attack down" is if they were to get wedged or stuck in a hole somewhere around the hatch.
Similarly they can't attack up, so if for example you're suspended above iron bars over an open ground, they'll just crowd under you while you hover. Some factors you've got to keep in mind is of the feral horde's weight that may be on your hatch, as that could cause it to cave in.
To answer your question though,even if the hatch appears to be on the ground, it still is using that one block above ground where it is placed.
So technically the hatches hit box is waist level and that's why they are able to hit it.
Just a quick tip, but digging at an angle until you hit bedrock is fairly effective if you can manage. By then, you'd be a long distance from your entrance. When a horde spawns, they want to go directly to you, where you're standing at. So yes, they'd be above you, but away from the hatch, which could prove to be useful.