Great charts, pacifishi. What does the "File Count / Upload" chart show? I'm not sure what its x axis is.
As for the formats, yes, they indicate compatibility. I know Format=2 is compatible with the last official KS release, Format=3 is KS Ex, and Format=4 is KS+. I don't know specifically which were the first versions to use Format=1 and Format=2 but I would guess you're right. The KS Ex editor doesn't automatically set the format to 3 when you make a new level, so I think that's why no levels declare that format on the archive.
Some levels use Format=2 to remain playable in vanilla KS while having extra features (like golden creatures) when played in KS+. Generally, KS+ doesn't disable features when playing a Format=2 level, but there are a handful of places where it has separate Format=2 and Format=4 paths in the code (such as in the screen rendering code).
Regarding the activity in 2018, someone uploaded 109 levels on June 5th, 2018. Most of them were pretty old, including for example most of Nifflas' levels. I think someone just wanted to upload all the levels they had that weren't already on the archive so they wouldn't become lost. Taking that into account, 2018 was comparable to other years.