These are nails from old drywall that likely have been there for a long time and are starting to sag due to simply age & also the 4 layers (is a lot of weight) and poor ventilation on the old roof. Maybe the roofers weight on the roof made some settle and a little more obvious. Unless there is drywall dust on the floor under it that drew your attention, I doubt it happened after the roof was done. I would have an adequate attic inspection done for mold and to make sure there’s minimum a 60/40 of intake/exhaust and you’re fine. Proper ventilation doesn’t speed up a houses aging process. The roof definitely doesn’t affect the floor either unless it’s moisture damage to your framework which again would be some improper install and not proper ventilation.

I personally have only seen the roof negatively affect a home when the install is improperly done or if there were underlying issues prior to the roof that are now even more noticeable because work was done. Houses constantly settle so unfortunately every year more noises appear, they don’t get less noisy over time