The Dictionary of Catch Phrases states that the original form of "You know what thought did?" is:
What did thought do?
and was exemplified in 1738.
LADY ANS: I thought you did just now.
LORD SP: Pray, Madam, what did thought
It's also seen in Lincolnshire Traditional Sayings And Proverbial Expressions.
When a child says "I thought so and so" the adult may respond with, "You know what thought did? He only thought he did." A teenager, however, may reply, "Ah, but when he looked he had!"
-a riposte which has the effect of counteracting the adult's attempt to control behaviour.