I'm in the middle of an Exchange 5.5-2003 migration, with one of each server in each of two sites. I'm running ADC on the Exchange 2003 servers themselves, and have had no problems related to it (directory syncs between AD and the 5.5 directory seem to be working fine). The GC servers used by both instances of ADC are on separate servers.
You probably know this, but once you're rid of your 5.5 servers and have switched Exchange to Native mode, you'll be shutting down the ADC for good. Just make sure you don't install Exchange 2003 on a domain controller, unless you want that server to be a DC forever (or if you want to take your chances demoting it, which I wouldn't recommend).