Light Shafts in the Caves would be holes on the overworld, in the same shape. These matching ones would be linked.
Rain:
When it rains, it will rain through the light shafts ONLY. When the rain has reached a point that an unprotected player would have 100 Wetness, the caves will start leaking through. When the rain ends, it will be the period of time that a player would go back to 0 from 100 that it still leaks, but the shafts don't rain, naturally. Then the caves would stop leaking too.
Weaponry and convenience:
People would be able to throw and put things in the holes, and they would fall down in the Light Shafts. If they hit a player, it would be equal to a hit in an earthquake. This would be especially cool if combined with things like Throwable spears, or Coconades.
Earthquakes:
I'm not exactly sure how these would be linked, but potentially when a giant is stomping around there could be an earthquake in the caves.
Enemies:
Dumb enemies would be able to fall in the holes (spiders, 'doydoys', volt goats, etc.)
Perhaps some enemies could actually use the holes for their attacks. For example, Krampus could dump stuff in them, or another boss could throw rocks and things down, especially if something or someone is there.
If it is possible, perhaps the holes could actually show what is down there in the day. Like, if a base is there you'd clearly see it and the people roaming around. But that would be pretty crazy.