Haven't been on Reddit for a few months but usually that happened in subs with strict rules on staying on topic / being serious like say /r/science. So a top level joke would lead to that whole comment thread being deleted.
Huge chains of lulz deleted (you could get that shit on any sub) but the several hundred word, amazingly detailed answer was the reason to visit askhistorians.
They at at least did it for a reason and their rules were clear. On many other subreddits comments would get arbitrarily removed just because the mods don't like them.
Its a reasonable theory. altho it sounds like it would create partially to mostly deleted comment chains and only occasionally fully deleted ones. (Im not on reddit anymore and have npt looked at their comment sections lately. If i missed somthing, let me know)
Because of power tripping janitors. See for instance any thread touched by awkwardtheturtle, the misandry-spewing cryptid who hates men because their ex-wife transitioned to male.