We all know the game gets very hectic in the later stages of a run. There's so many things going on in the screen. A visual indicator similar to weapoon/passive pickups should help a player know if he already killed a boss. This would be a big help when unlocking secrets that require you to kill bosses.
#Boss Indicators
coral elk
hexed hatch
Maybe bosses could be foreground elements? In addition to making it easier to tell what bosses you have killed, it would also make bosses stand out more compared to other enemies