Honestly, I think it's an advantage at this point. Way too much diversity to easily attack remotely.
All the ones I've encountered in the wild ran VxWorks
Ostensibly yes, but so far I haven't seen anyone really use a PLC in a way that requires hard real time (so far). The cycle on eg a siemens S7-1200 is anyway much too slow for anything really exciting, and a Pi might very well be more reliable in actual practice, were it not for the very unfortunate tendency to eat SD cards. :-P
(And revolution pi actually ships a hardened Pi for industrial use. So that's one way to go about it. I'm not a big fan of that brand, but it's a data-point. Meanwhile in personal experience some regular pi's left in industrial cabinets for one-off emergency monitoring purposes have managed to stay annoyingly alive over time.)
Now, if you really want to use rpi as a plc, you need something like openplc or codesys as a runtime, add some HATs for I/O, and use protocols like modbus. It will be a software plc but you are missing the hardware certification and other features. Rpi is good as edge computing rather than plc, like processing vision or data logging, it’s why in drones you need the autopilot AND rpi or companion computer, each does certain functions.