Great Old One
That's not how I would rule it. Dim light only imposes disadvantage on Perception checks that rely on sight. I wouldn't have that disadvantage cancel out the advantage on Perception checks that rely on hearing. So I would say that the owl might be able to hear something without being able to see it.
Maybe I was not clear (because I wrongly mentioned smell instead of hearing in the post), but it's exactly what I meant.
(I'm willing to be nuanced about Perception -- treating sight, sound and smell as separate things.)
So am I, just made a switch between smell and sound in the post.