iMessage sync with the computer?
What happens in your proposed case is that if you delete messages from the iPhone, and then power on your Mac, the Mac will not receive those deleted messages.

EDIT: Well, folks, I stand corrected. I certainly believed the above to be the case, but my tests proved otherwise. I sent several messages from multiple devices to other devices that were powered down. Each message was deleted before the recipients were powered back on. Although there was a significant lag in reception (one took nearly ten minutes), all messages that were sent were received, even those that were deleted.

Several of the messages were out of sync, which doesn't surprise me given the flakiness of the iMessage system during its infancy. However, to the original question, the answer is that messages, deleted or otherwise, eventually find their destination, even to devices that were powered down when those messages were transmitted.

(Hat tip to tubedogg for the correction.)