Both feet on mine. Hands as well. There's even the caption "Left Foot", "Right Foot" underneath each one which I always thought was odd, as if we couldn't tell the difference! My take is that this was done mostly for sentimental reasons, I don't think it was intended for ID'ing purposes. Heck, maybe it was done simply to prevent hospital staff from inadvertently switching babies on sedated mothers.
As you imply, this was done at the hospital and does not appear on the official birth certificate issued by the state. I have no idea if the state keeps a copy of those footprints or if it's restricted to hospital records.