do the little scratches the come from hanging lures from the rod holders damage or weaken the rod in any way???

Scratches can and will weaken the blank, but since the hook keepers are so far down on the rod, I highly doubt you'd see breakage from a hook scratch. I know I've never seen a rod broken down that far. Now put that same scratch about midway up the blank and you've got a potential problem.

Depends if the scratches are actually into the lacquer around hook saver or blank, cosmetic lacquer scratches will not weaken blank.

A cosmetic scratch means nothing, if the scratch is into the blank, problems could arise.

60 years of fishing, never used a hook keeper, my lures are always on on the bottom guide. No scratches, no damages, no nothing to be concerned about, if I were concerned my hook would be on the crossmember of the guide and not the insert, but I'm not concerned. Can't recall ever having a scratch on the bottom guide inert where the hook is hanging. Only thing I would be concerned with is a safety factor, I don't want a lure flying off the guide, if the reel is cranked too tight( with a bow in the tip, that's dangerous) too loose and it only falls off, no danger. Keep the right tension with no stress on the tip and you are fine.

Unless the graphite fibers are compromised you're safe. Scratches in the finish are just cosmetic. A more likely scenario is broken fibers caused by a Carolina weight flopping around during transport. Damage can be hard to see until it's too late.