Hi Tom,
I don't think that slate will be a problem for pymy corys. Slate is generally in rather large slabs, isn't it? The surface is smooth. This should be fine.
I have some pygmy corydoras and they don't spend very much time scouring the bottom, anyway. Not like my other corydoras. They sometimes even school with my harlequin rasboras or sit on leaves. They spend more time in the mid and upper levels of the tank than my other corydoras, which tend to scour the bottom.
The main thing I'd worry about with slate (for any bottom dwelling fish) is whether it has sharp edges. Corydoras, like some other fish, can startle if the lights go on suddenly or if there's a sudden movement near the tank. At that time, the fish can dart around briefly in alarm. If the edges of the slate are sharp, they might injure themselves on the slate.
If you have gravel in your tank, I'd recommend burying your slate's edges in the gravel. That's what I've done in my corydora tank, and the corydoras have enjoyed nibbling food off the slate. Their barbels are fine and they seem to like the slate even better than the gravel. (They're not pygmy corydoras, though; the pygmy corydoras are in my other tank.)
If you can't bury the sharp edges in gravel, perhaps you can either buff the edges or just pick your pieces of slate carefully.
I hope that you post pictures!