Your phone has to be informed somehow, from the internet, that it has data to present as a notification. The fact that you got a notification at 3:32 and then again at 3:35 is trackable data, pretty much no matter what anyone does with it, encrypted or not. Doubly so if someone has MITM attacked your data stream. They may not know what the notification contains or even what app it was sent to, but the act of transmitting and then receiving this data packet over cell network or internet is a trackable event. And I don't really know what Apple could even do about that beyond attempting to build Internet 2 solely for the purposes of keeping the cops out of it, which is unlikely at best.