As per discussion in Slack: https://r3dlg.slack.com/archives/CCKJR4MFT/p1550859067152900
net.corda.core.messaging.pendingFlowsCount has been moved to net.corda.nodeapi.internal.pendingFlowsCount
... and pendingFlowsCount is not currently in api-current.txt on master
however, pendingFlowsCount is in api-current.txt on the V3 release branch
it seems like this (see link below) is the point in which it got removed from master, and thus "disappeared" from the public API. Michele later moved it into an internal package, which didn't get picked up by the API checker for that particular reason.