That's a common misconception. When we had a problem with the nylon nuts on the P-3, the first thing my boss suggested was all-metal nuts. Checked the Mil-spec and found that they were rated for a much shorter life than the nylon nuts. Took it to the lab and found out that the spec was right.
Of course this was with mil-spec nuts procured to an MS number. It might be that the ones that one buys from hardware stores that do not specialize in MS and aviation-grade fasteners might not last as long.
Yep. Was a real pain--some genius had designed the thing with flat-head Allen bolts, which have a little tiny recess compared to regular socket-head cap screws. So they'd go in all right but trying to get them out after they'd been torqued the wrench stripped the hole every time and they had to drill. Fixed it with dry-film lubricant (I forget the brand now--it was 20 years ago).