Re: Can I use "which" after the subject when it's insect or animal?
Yes, it is.
However, I would rephrase the sentence, make it simpler: "The owl is a nocturnal bird."
And about "the": if every species of owl is nocturnal, then it is all right. If not all are, you should mention it: "The owl is a nocturnal bird, except the _____ and the _____ owls, which can be seen both at night or during the day." (just an example, not that I actually know anyhting about owls)
Please be aware that I'm neither a native English speaker nor a teacher.