Writing on the word nincompoop, Anatoly Liberman (Word Origins 111) says
... At one time, nickumpoop was more offensive than it is now and may have referred to a certain Nickum, a notorious poop. Weekley suggested that Nickum is Nicodemus, mentioned in John III:1-4. Nicodemus, "a man of the Pharisees," came to Jesus by night and confessed his faith in Him. Jesus responded that "[e]xcept a man be born again, he cannot see the kingdom of God. Nicodemus saith unto him, How can a man be born when he is old? can he enter the second time into his mother's womb, and be born?" Jesus did not answer the question directly but repeated: "Ye must be born again" (the quotations are from the Authorized Version).
The nocturnal interview did not do Nicodemus any good in the eyes of posterity. He gained the reputation of a blockhead unable to understand the simplest things and became a popular figure in medieval mystery plays. Modern French nicodIme means "simple-ton:". Some time later, nickumpoop changed to nincompoop, perhaps under the influence of ninny, a sixteenth-century word for "duffer," supposedly from Innocent, by misdivision, like Ned and nuncle from Ed and uncle.
In Weekley's opinion, ninny and its synonym noddy are traceable to Nicodemus's name; to boost his hypothesis, he cited noddypoop, another word for "fool:' (Nor did Nicodemus fare better in later times. The French family name Nicot goes back directly to Nicodemus. Jean Nicot, French ambassador at Lisbon, introduced tobacco into France in 1560; hence nicotine.)
In deciding whether to accept an etymology, we usually have to weigh probabilities. Someone called Nelme comes from a family that once lived "at an elm:' By contrast, nincompoop cannot be shown, beyond reasonable doubt, to derive from Nicodemus, rather than from, for instance, Nicholas or Old Nick. Weekley's conjecture is good, and that is all we are allowed to say. The Oxford Dictionary of English Etymology agreed with it, but Skeat did not, and most modern dictionaries say the meaning is uncertain.