There is no 'literal waterboarding scene' in the theatrically released Shrek. In the scene you've seen, unless you're deep into dubious fan-remakes, Gingy 'just' gets dipped in milk (mostly off-screen) by an executioner-style heavy, then Lord Farquaad taunts them with their torn-off legs, which suggests legs-first dipping, not the head-first submersion that is the entire point of waterboarding.
Still pretty bad (even though the gingerbread buttons were apparently spared), but... not literal, and not even figurative, waterboarding.
Still pretty bad (even though the gingerbread buttons were apparently spared), but... not literal, and not even figurative, waterboarding.