What are some examples of questions that at first seemed stupid yet became brilliant when connected with other seemingly stupid ideas?
A lot of early work into physics seemed like dumb questions at the time. When taken to the extreme “Do heavy objects fall faster?” tells you quite a bit about how the world works. And critically people intuited the wrong answers to many such questions before careful experimentation.
My understanding is that much of discrete mathematics was considered to be purely academic until computers were invented.
Microwaves were invented as hamster defrost machines. Seriously!
Rather than a singular "question" that seems stupid, consider prime numbers. People toyed with prime numbers for centuries, asking all sorts of questions, with little-to-no impact on the vast majority of humans. Fast forward to the age of telecommunications: suddenly massive innovations in cryptography are being built on knowledge of prime numbers that previously was a novelty.