Ignore me, I was getting the major compaction for LCS mixed up with STCS. Estimated droppable tombstones tends to be fairly accurate. If your SSTables in level 2 have that many tombstones I'd say that's definitely the reason L3 isn't being compacted.
As for how you got here in the first place, hard to say. Maybe a burst of writes over a period a long time ago? Or possibly repairs streaming a lot of data? Hard to tell what happened in the past without lots of metrics.
