I lodged a support ticket with the Microsoft Entra/Azure support team and received an answer from them around an hour ago to say that Microsoft was aware of the issue and they believe it is now resolved. They said that the problem was "Due to a recent rollout of a design change of Microsoft Entra Connect Health agent, the agents installed in customer premises started getting throttled by Service"
Hopefully these alerts stop coming now. I haven't received any alerts for just over 12 hours now, so it is looking promising.