I've read the entirety of The Knights of Bushido; I don't recall any references to waterboarding.
It is hard to respond to your line of thinking in a favorable way. I refer you to an segment of Wikipedia’s waterboarding article:
All special operations units in all branches of the U.S. military and the CIA’s Special Activities Division[148] employ the use of waterboarding as part of survival school (Survival, Evasion, Resistance and Escape) training, to psychologically prepare soldiers for the possibility of being captured by enemy forces.[149] John Yoo, former Deputy Assistant Attorney General under President Bush stated that the United States has subjected 20,000 of its troops to waterboarding as part of SERE training prior to deployment to Iraq and Afghanistan.[150] Dr. Jerald Ogrisseg, former head of Psychological Services for the Air Force SERE School has stated in testimony before the U.S. Senate's Committee on Armed Services that there are fundamental differences between SERE training and what occurs in real world settings.[151] Dr. Ogrisseg further states that his experience is limited to SERE training, but that he did not believe waterboarding to be productive in either setting.[152]
Jane Mayer wrote for The New Yorker:
According to the SERE affiliate and two other sources familiar with the program, after September 11th several psychologists versed in SERE techniques began advising interrogators at Guantánamo Bay and elsewhere. Some of these psychologists essentially “tried to reverse-engineer” the SERE program, as the affiliate put it. “They took good knowledge and used it in a bad way”, another of the sources said. Interrogators and BSCT members at Guantánamo adopted coercive techniques similar to those employed in the SERE program.[153]
and continues to report:
many of the interrogation methods used in SERE training seem to have been applied at Guantánamo.[153]
However, according to a declassified Justice Department memo attempting to justify torture which references a still-classified report of the CIA Inspector General on the CIA’s use of waterboarding, among other “enhanced” interrogation techniques, the CIA applied waterboarding to detainees “in a different manner” than the technique used in SERE training:
The difference was in the manner in which the detainees’ breathing was obstructed. At the SERE school and in the DoJ opinion, the subject's airflow is disrupted by the firm application of a damp cloth over the air passages; the interrogator applies a small amount of water to the cloth in a controlled manner. By contrast, the Agency interrogator ... applied large volumes of water to a cloth that covered the detainee’s mouth and nose. One of the psychiatrist / interrogators acknowledged that the Agency's use of the technique is different from that used in SERE training because it is ‘for real’ and is more poignant and convincing.[154]
According to the DOJ memo, the IG Report observed that the CIA’s Office of Medical Services (OMS) stated that “the experience of the SERE psychologist / interrogators on the waterboard was probably misrepresented at the time, as the SERE waterboard experience is so different from the subsequent Agency usage as to make it almost irrelevant” and that “[c]onsequently, according to OMS, there was no a priori reason to believe that applying the waterboard with the frequency and intensity with which it was used by the psychologist/interrogators was either efficacious or medically safe.”[154]