To understand the cause of under replicated partitions, we need to know more about the Stream nodes cluster on this environment. If the Stream nodes are restarted frequently, it can lead to NORMAL nodes reporting under replicated partitions.
It is correct that in Pega 8.x, Kafka is enabled by default. There are a few internal Kafka topics used by Queue Processors, as well as, there can also be custom Kafka Topics created via Stream Datasets in the platform. Each stream will have it's own dedicated topic.