Unity 3.x handles hidden recipients by default, however some builds of 2.4.6 require a registry edit for this to work properly. You also need Exchange 55 SP3 or later I think... You can go ahead and download the latest version of the Advanced Settings Tool from AnswerMonkey here:
http://www.answermonkey.net/App_AdvancedSettingsTool.htm
run it and select the "Show Hidden Subscribers" and "show Hidden Distribution List" options on the left. If you set them both to 1 and restart Unity you should be good to go.
That said, if these keys were not set and you hide a user in the address book, you'd be seeing more problems than just the MWI working (i.e. they wouldn't show up in the SA after a while)... so I'm not entirely sure this is your problem but it's worth checking.