The most likely cause is that the HBase Canary (part of HBase, not from Service Monitor) is pinging each region's health regularly.
Prior to CM5.3.2, turning this HBase Canary off didn't work. So you could either - upgrade to CM 5.3.2 (or later). This should not lead to cluster downtime as only CM and agents will be upgraded. - lower the frequency of the the HBase Canary so that the discrepancy in stats is reduced.