I believe this is available via CallControlAddress.getMessageWaiting().

Correct, getMessageWaiting() throws a MethodNotSupportedException.

Since DevSupp engineers are reading these forums quite often I wonder.. is there any chance we could see a more complete JTAPI implementation in the future? It's always frustrating when you run into a situation that JTAPI covers, but Cisco's implementation does not and you have to either give up or develop some extensive workaround (one of my favorite examples are media capabilities.. whether you can simply play an audio file or have to set up rtp streaming via jmf.. there are worlds in between... or you cannot use an RP for media even though I think it would be predestined because it is designed to handle large number of calls whereas the CTI port isn't).