What size screw to use with IBM NetBay clip nuts or cage nuts

Never heard of that "thread making screw" procedure (which isn't to say it doesn't exist, but I've never seen it).
Most racks will have an earthing lug on them - Just bolt the PDU's rack ground line to that & you're all set (as a bonus that lug is usually bonded to all the metal bits of the rack so you're guaranteed to be grounding everything that should be grounded).

As to whether the grounding is necessary, it's certainly a good idea (If something goes catastrophically wrong and mains power somehow gets shorted to the rack rails this gives it a better path to ground than "via the datacenter technician's body"). Necessary may vary according to local codes, but I would definitely recommend it.

There's no precise M5 equivalent but I think you'll be fine with either a 10-32 or 10-24 depending on TPI, they're cheap so just buy both and be careful with the first one. No idea on a supplier in NL though sorry - oh and consider changing out the four mounting poles to square ones - they may not be too expensive and would mean you wouldn't have to worry about this problem again.

Good luck.