I'm in this boat too. Whatsapp seems to be the biggest culprit & since updating to iOS 9 last week they have been very hit & miss. Everything switched on as per pre update , but now they either make no sound at all , or just when it feels like it. Also I've noticed when I'm in whatsapp , & another message comes through via the drop down notification , it doesn't make a noise now. I checked my whatsapp settings & see the in app setting has gone , so I guess this is a whatsapp doing. That aside , my first problem is certainly happening as per the OP , notification sounds very irregular. Whether an iOS 9 bug or Whatsapp bug I don't know. If the latter I guess it'll be months before a fix.
iPhone 6+
My partner has a 5S & has the exact same problem with whatsapp.
Cheers