If a thread is waiting on I/O (or deadlocked, or whatever) when you call exit(), I don't know what happens, but I'd guess that you're right--the thread just hangs around. The easiest way to end a waiting thread is to call interrupt(). If a thread is busy calculating pi to the last digit, it should be written to check a "please quit" variable somewhere that can be set externally. Unfortunately, there is no Thread.stop() method on BB.
Since there are no thread groups or daemon threads on BB devices, you might have to write your own thread manager to do all this. The manager would be told when threads are created, when they finish, and when the app is going to exit. For the last, it would go through the list of threads and calls interrupt() on each one that's still alive. This will work better if you write all your thread code to cooperate with the manager (for instance, to register itself with the manager and to notify it when the thread finishes).
If you have threads being spawned inside code you don't control, I don't have any good suggestions.
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