The best hardware setup I have used (WABTEC and GETS, end of train cars, so vibration is an issue) was unplated holes with a pad, SEMS hardware with a nylon patch applied (double locking mechanisms).  Fastenal offers this service, but I am not sure if they sub-contract it out or not.
The unplated hole was nice to avoid the potential for hardware scraping, the pad was nice for easier hole identification (operator aid), and the SEMS has all the right 'stack-up,' so it saves on having multiple part numbers to track down.
Cost differential of a screw, lock, and flat versus the SEMS was around 3 cents on average (small bump in price, but well worth it).  In helicopter applications, I am still required to strap the hardware, but have never (Knock on wood), had any hardware come loose.

As a CM, I flag designs that apply a lock washer directly to the PCB whether there is a pad or not.  I can usually get the customer to update to a SEMS.

The other advantage of the unplated hole with a pad is that if at any point a Press-Fit PEM(R) or other hardware is applied, any cracking that occurs (it always does), the copper pad limits the extent of the cracking.

Recommendation, have an unplated hole with a pad.  Reduce the pad diameter if needed, but the flexibility and advantages outlined, I feel, outweigh not having a pad on the PCB.