Hello,
I'm on SCOM 2012 R2 and have the Exchange 2013 MP (version 15.0.665.19). I am having the same issue where the following are not being monitored:
Mailbox Database Copy
Exchange IIS Application Pool
You and the documentation mention that the discovery rule is not enabled by default. However it appears that all the discovery rules are enabled by default in my version.
I can post pics if that would help.