I often make certain that a channel's file browser does not contain any files before I delete it. If it does, I move them to another browser (very simple task). The case is not the same, however, for other administrators of my server who are not as careful when it comes to simply deleting channels. I am not sure what happens to files in a certain channel when the channel is deleted. I am assuming they are deleted as well.
A nice simple popup warning an administrator who is about to delete a channel with files in it that halts the process and informs the person that "Wait a sec, there's files in this channel too that will vanish forever if you delete this channel!"
This is often overlooked.
Just an idea! Maybe you think this would be useful :-) Maybe not :P