I have seen it used.
The above OSHA link doesn't distinguish between a "PLC" and a "safety PLC".
The E-stop button, with appropriate underlying components, circuits, and logic is OK for preventing something within its span of control from "moving" under power if you lock it from being released. If that's the purpose for which the lock-out is being applied (e.g. to service mechanical parts of the system), that's one thing. It's quite another if someone is doing electrical work. It will NOT prevent electricity from being supplied to the panel that contains these components, and possibly not stop electricity being supplied in some form to the motor (just not necessarily in a form that will cause the motor to rotate - see "safe torque off" on a VFD or servo drive, for example).
Local standards and locally accepted practices may dictate otherwise.
If locally applicable standards permit the use of a padlock over an E-stop button then at a minimum the written lock-out procedure (you have one, right?) needs to distinguish between performing mechanical work and performing electrical work.
Ultimately there is no substitute for the big ole' disconnect switch with a padlock on it.