Is believing that the harm of some modern medicines outweighs their benefit, then rectifying this belief by remembering that benefit and harm are solely in the hands of Allah the Almighty, considered polytheism (shirk)?

There is no harm in saying that the damage of something outweighs its benefit. This does not mean that the thing benefits or harms by itself, without Allah's decree, or that it is the creator of harm and benefit. Allah mentioned this regarding intoxicants and gambling in His saying: {and their sin is greater than their benefit}, and regarding those who invoke others besides Allah: {He invokes one whose harm is closer than his benefit}. Similarly, it is mentioned in the Prophetic Hadith about seeking protection from Satan when approaching one's spouse, that whoever does so, "Satan will not harm him," and this does not mean that Satan harms without Allah's decree or that he is the creator of harm.