[Shub-Nigurrath]

it's enough to hide the watermark in the instruction execution flow or in the data structure to create an almost impossible to un-watermark program, but there are hundred different ways to software watermark a program. Watermarking if properly done is one of the most efficient protection strategies (of course you must assume, like for IDA, that users can be threatened removing their licenses, if you catch their leaked copies on the net): it's easy to implement and doesn't complicate development, it's quite difficult to completely remove it.