That said, it would make sense to provide slight clues if you're creating a simulation to test what it would take for the civilization to realize that they're simulated.

Exactly. I mean of course they could allow us the luxury of wondering about it. I mean I would, if I were part of the people running the stimulation.
It's fun, isn't it? Let us give em a clue or two here; or just make them wonder, fortuitously and fruitlessly.

Cos Like @full-measure said, I doubt we could ever come to an absolute hundered-percent-certain conclusion that we are in a simulation. So why not leave us the capability- through a hint or two here and there- to wonder, aimlessly, if we are.

It's genius, IMO.