There are essentially two ways of retuning a shakuhachi. One can rework the bore, but for obvious reasons this is impractical. That leaves moving the holes. Many players simply have the holes redrilled lower down, though others, myself included, prefer to have the holes angled down towards the inside, which accomplishes the same goal without marring the outside of the instrument. I have been taught the procedure by a professional maker, who has seen my work and approved (actually, commended) it.The vast majority of shakuhachi are not in tune with the western diatonic scale. The note "chi" is usually the sharpest, and often "re" and even "tsu" are sharp as well; however, it is not rare for "tsu" to be flat, and "ri" is sometimes sharp or flat too. Furthermore, the upper, or "kan" octave is often sharp in relation to the lower, "otsu" register. Thus, when I retune a shakuhachi, I often do not lower at least the chi hole all the way so that it is exactly it tune, and I generally do not raise the pitch of a note by moving or opening up the hole, as it is necessary, I believe, for any player to become used to making adjustments in pitch while playing. Since many factors involving the player him/herself affect pitch, developing an ear for pitch is an integral part of learning to play. Also, a sharp "chi" makes playing the note "san-no-ha" much easier, and it is possible that makers in the past had this in mind, though it's more likely that the holes were merely spaced evenly without consideration of pitch, as that is what one finds on old flutes.
In any case, I advise against choosing only flutes whose every note is perfectly in pitch. First of all, such flutes are extremely uncommon, even among modern shakuhachi. Second, as long as a flute is not so far out of tune that compensating for it is very difficult, one should base one's choice on other factors, like ease of playing, tone color, and so on. Last, I've found that some players will play shakuhachi to their tuner and decide it's too out of tune, but when they play without the tuner their playing is more out of tune--their meri notes are quite sharp and/or san-no-u is flat. Thus in my opinion a difference of less than 15 cents is not problematic, as one can compensate for most of that easily, and the remainder will not be noticeable. If you check the playing of even the great Japanese masters you will notice that their pitch varies at times by about this amount.
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