You DID need to connect the controller EVERY TIME there was an update, whenever the PS3 restarted after the update - it would not complete the update until the controller was connected via USB. I have had my PS3 since they came out and this was always the case until about 4-5 months ago. It was in the official release notes for whatever update it was that said you no longer have to have a controller connected via USB to complete the update, and I remember it distinctly because it always bugged me that you had to connect it for no apparent reason other than confirming the on screen actions. If you've had it for that long, you would have experienced this too, so I don't see how you can say otherwise?
With the other controllers that I connected to mine, both had been attached to another PS3, so in order for them to communicate with my PS3, they HAD to be connected, once they were seen, they worked wirelessly just fine. Otherwise, it would just sit there and flash looking for the PS3 that it thinks it is connected to, like any BT device would when it was out of range.