Will the moving spike balls from Pezrock and spikes from Exoticus be removed from the enemy count? I think one of the Exoticus levels has an unreachable enemy anyway, but counting spikes and environmental hazards with a ton of HP as enemies doesn't feel right.

Levels I know of or remember, where it's impossible to get 100% are:
Tubelectric 2
Nippius 2 (unless you cheat with a hoverboard)
Jungrock 1 & 2
Sluggion 2 (thanks to the unreachable section of the map)
Dreampipes 2 (unless you use cheats to get dynamite for the last 2 unreachable enemies)
Battleships 2 (unless you use a hoverboard)
Exoticus
Rainforus (not sure if you naturally get dynamite or have to use cheats, but without them, certain enemies are almost impossible to get)

also, unless the GOG version messed something up, I don't remember either Deserto levels being impossible to get 100%
I clearly remember getting all items and kills in those levels (though I was playing the version that has the extended Tubelectric 2, properly functioning Orbitus 2 level, broken Marbelara secret level and has the invisible spring removed from all levels they were in