It is not 100% clear - like Missingno in general - but logic and evidence suggests that the developers gave it its name.
Missingno isn't a real glitch Pokemon, in that it was (most likely) an intentional addition by the developers. Missingno. is, based on everything we know, a placeholder for the 39 remaining index numbers that aren't occupied by the real 151 Pokemon. There are 190 index numbers, and since only 151 of them were actual Pokemon, there were 39 left behind that became Missingno.
It is not known for sure if the developers originally intended for these 39 slots to contain Pokemon, but according to a Smogon user who claims to have had a discussion with Shigeki Morimoto, there were supposed to be 190 Pokemon, but some were "saved for later."
It would have been silly to leave the game to make a junk name for the spare 39 spots, so the developers named them Missingno, or けつばん aka Ketsuban.