I've seen a combination of both, the PLC will:
1. drive control relays (due to the contact rating of the plc's built in relays) and,
2. perform all the logic, annunciation functions
Make sure the logic is failsafe (e.g. if it is driving lube oil pumps: the pumps run when the system is tripped (control relay is DOTR - dropout to run), the only way to stop the pumps will be to open the MCC breaker, if it is driving fuel-oil pumps the control relay MUST be PUTR (pick-up to run) otherwise you'll be pumping fuel into you-do-not know-what...
The thunderstorm problems I had were always troubleshot to poorly installed shielding and grounding system.
HTH
Saludos.
a.