Does placing cotton in a perforated tooth affect the validity of the fast, knowing that water will penetrate it during Wudu (ablution)?

Your filling your tooth with cotton while fasting does not invalidate it, even if water penetrates the tooth. The important thing is that you do not intentionally swallow the aforementioned water. Assuming some water unintentionally reaches your throat, your fast is valid, and there is no blame upon you.