You're right about the data going over the microwave backbone systems for site monitoring, but sometimes on smaller systems it's done on a talkgroup instead, or a combo of both. That's because that type MOSCAD setup reports only "exceptions" to system operating parameter. Once the "exception" is acknowledged by the terminal operator, it does not repeat the data. "Exceptions" would be alarms and other devices that provide simple contact closures in their alarm modes. This type of data produces very little traffic.
Flow meters and pH monitors and other instruments with continous analog outputs regularly "report" over the system either by a predetermined interval, site polling, "exception" (alarm) reporting, or some type of rate-of-change monitoring. Most systems utilize a combination of all those.
Many times when designing new trunking systems, we add talkgroups for data only that relay site monitoring data, storm water monitoring data, water/sewer data, mobile data, security data, remote video frames, etc, etc to their respective destinations. For data sites that aren't located at a microwave interface, we use the SCADA's "store and forward" capability to forward its data to another site that is microwave interfaced, and you'll hear that traffic passed over the trunked talkgroups to the MW site where it enters the backbone system. There are MOSCAD setups that will have a chain of several sites storing and forwarding data to a relay terminal site over simplex or spread spectrum freqs because the sites are not able to hit the repeater or receiver sites on their own, and the relay terminal site then relays the data over the trunked system or MW to the intended destinations.
In other words, the new digital trunked systems don't just handle voice and mobile data traffic, and they are much more complex than most people know. Just as a heads up, on digital systems what you may hear that sounds like a digital control channel but your scanner won't ID as such may be one of the digital SCADA talkgroups. You're not crazy and neither is your scanner. If you hear it as FSK and you hear it in short bursts, it's analog SCADA.
Hope this helps.