I just had this happen on my save, Winter 17 (+/- 1 day) Year 3. Do you have the mod Weather Wonders? I did a code dive into this mod's files; here's what I found.
- WW is dependent on MoreNightlyEvents (a framework mod).
- the WW Nexus page confirms the existence of a nightly earthquake event (under Features). How does the event behave?
- There is a nightly event ([FTM] Weather Wonders -> content) that seems to spawn ore nodes in the quarry (could also be the quarry on your farm, if you chose that farm type (I think)); in-game verification is inconclusive.
- This event also has EarthquakeSound.ogg ([CS] Weather Wonders -> assets) which matches what I heard during the overnight event.
- I can't find the text "intense earthquake" in WW's files, it's probably buried somewhere that I haven't looked.
- According to ([CS] Weather Wonders -> Data -> Nightly Events -> Earthquake) I also should have received a mail about this event, but I did not; I'm guessing that's a bug, but i'm not certain.
If you don't have Weather Wonders, let me know and we can compare mod lists.