Resources spawn according to a pre-defined (at world generation) chunk density.
If a given chunk has something like 10 gems, 15 hard coal, 15 fossils, 30 iron, 10 gold, 10 flowers and 5 mushrooms, and 5 boulders it’s going to respawn resources according to those percentages.
So if someone comes through deep and mines 50% of those minable resources (50 items), the regen is likely to also regenerate some surface resources, as it will regenerate something like this:
10% gems = 5(ish) gems
15% hard coal = 7(ish) hard coal
15% fossils = 7(ish) hard fossils
30% iron = 15(ish) iron
10% gold = 5(ish) gold
10% flowers = 5(ish) flowers
5% fungus = 3(ish) fungus
5% boulders = 2(ish) boulders
Now since it was a miner that came through and it was 50 underground resources taken, you can see that after regenerating 50 random resources according to the initial chunk density - the chunk will have flowers, boulders, and fungus added during the respawn.
If nobody ever surface gathers here, and miners come through occasionally, the surface resources in the chunk will grow denser over time, and the mined resources will be unable to spawn back to their original densities.
This is how a hot spot gets “thinner over time”. It’s a good idea to go surface gathering around your favorite mining spots, or mine under your gathering spots, from time to time because of it.
Edit:
Here’s a random thread about some tuning that was done aroudn the release. It’s a fair jump off point if you still want more details
It says full regen of a given chunk was happening in roughly 85 hours at the monitored places.