I've definitely experienced that in the past, spanning 10.10 -- 10.13.6, so I don't think it's a Mojave thing. Sometimes the enrollment profile goes away, sometimes it's other profiles that should be in scope based on tags remove themselves.
I never found the root cause, but I got the problem to not reappear:
1- uninstall the Meraki agent
launchctl unload /Library/LaunchDaemons/com.meraki.agentd.plist
rm -f /usr/local/sbin/m_agent /usr/local/sbin/m_agent_upgrade
rm -rf '/Library/Application Support/Meraki/'
rm -f /Library/LaunchDaemons/com.meraki.agentd.plist
2- (requires physical access to the Mac) boot into the Recovery partition and disable SIP. After the Mac reboots back into the Recovery OS, remove the configuration profile database. Then re-enable SIP.
csrutil disable
-rf /var/db/ConfigurationProfiles/Store/
csrutil enable
3- Then re-install the Meraki agent/re-enroll as needed