E-ki's first impression of their death was probably wrong. D-suke was skilled with handcrafts, and he could easily been talked into making replicas of say, dead bodies, for the sake of a more realistic movie. Whoever did it, didn't kill all of them there, just deceived, threatened, maybe even injured them there in order to make them comply. What the teacher found there weren't their actual bodies, hence there couldn't have been a luminol reaction, while the blood on the floor was most likely E-ki's. Whoever did it just convinced them to leave the school or abducted them, then killed them afterwards.
And as for who was it, B-ka was the first to go missing, and the last lines said to E-ki strongly implied it was him. Assuming he stayed tiny after becoming an adult, or that he's even male to begin with, he also has the physique to disguise himself convincingly as B-ko, years later.