It is true that the inventory data will be stored in a separate database; however, reports, by default, read from ALL Management Groups, so there would be no impact to your existing custom reports. Only if you wanted to filter those reports by domain would additional customization be necessary.
In fact, because the report would be reading from two different Management Role servers (i.e. databases) simultaneously, the reports will actually render faster than they would if all of the data were in a single Management Group database.
