Neither is correct, actually. 1) You don't put the time of the event when you use present perfect. If you use a time, then change the tense to past simple. 2) Past perfect cannot be used to describe now. You need to give us another past event for the past perfect sentence to function. Again, to fix the sentence you need to use past simple tense.

The time is mentioned so you have to use simple past tense according to the idea you want to express. You can simply say like this "he replied to your email this morning about 9 A.M. NOTE: If you want to mention another event in past in same case, then you can say like this " when we checked our mail box at 10 A.M, we found that he had replied this morning at about 9 A.M. ( Past perfect ) Furthermore, if you don't want to mention any time then you can simply say " he has replied to your mail." Hope it will help you.

"Has" sounds more correct, but honestly, you can just leave out the "has/had". If someone is asking if their email has been answered, you would just tell them "Yes, he replied to your email this morning about 9 AM."