With the SCT, if you leave your truck tuned it will be detected (duh) but if you set it back to stock before you take it in, it will set a "hidden" code that does not turn on the engine light. However, this code is the same one you get for disconnecting the batteries for any length of time. It has something to do with the computer erasing the history from itself (can't remember the exact number or description at the moment). This code will clear itself after several driving cycles, after the computer has re-learned everything.
So the over all answer to the question "can a tuner be detected" as far as I know, is no. But there are several items that can lead a dealer to suspect one has been and therefore give probable cause. Such as the memory code, a few connectors cleaner than the others (meaning they have been tapered with by means of an external box), sensors installed for gauges, etc. I know on the 7.3s dealers would look at the pins on the computer to see if they were extra clean to tell if a chip was plugged in. It's a risk you take if you want to tune your truck.