RIM probably does what they can to build reusable code into the OS to eliminate code bloat, maintain UI consistency, simplify debugging, etc. My guess is that they have defined a number of java objects that support messaging functionality in general -- e.g., a two-party user interface, display of a two-party conversation, threading, etc. These might look a bit different in BB messenger or SMS, but it's quite possible that RIM uses a bunch of common code to support the two different applications since they're so similar.

If that's the case, then it's quite possible that the code that handles threaded conversations for both BB messenger and SMS will be delivered in the COD files that make up the upcoming version of BB messenger.