Article mentions that the aircraft also provides GPS-based speed, so maybe that's how? That's just an educated guess, I have no real idea.

Edit: Reading through the official investigation document:

"The angle of attack is the parameter that allows the stall warning to be triggered; if the angle of attack values become invalid, the warning stops. "

So like said in another comment - even with no valid speed values, the angle of attack can trigger a stall warning.