How can one achieve complete certainty regarding the supplication's response, while acknowledging that what is supplicated for might be evil in Allah's knowledge, and without that affecting the degree of certainty?

One must be certain that whatever Allah decrees is good and in one's best interest, and to entrust the matter to Him, Glorified be He. Supplication is good, whether the response is granted immediately or delayed due to divine wisdom, for a Muslim never loses out by making supplication.