There are many differences between ji-nashi flutes and flutes made with ji. But then, there are also an infinite number of differences between all of the flutes that are made with ji.
In other words, it’s hard to generalise. Many people (including me) think that excellent ji-nashi flutes are very desirable. But this might be a personal preference thing, rather than something based upon concrete and consistent observations. Among the subjective words I might use to describe the sounds a good ji nashi flute makes are ‘mellow’, ‘responsive’, ‘rich’, ‘smooth’, ‘traditional’, ‘complex’, etc. Note that none of these words really describe the actual physical sound, but we all think we know what they mean. At least we know what they mean to us!
This may be one of those things that if you can’t tell the difference by yourself, when playing on the two types of flutes or listening them being played, then there is no point really in hearing someone else’s opinion on the subject.
Generalising about pitch or intonation might also be counterproductive. The quality of intonation varies between all flutes, whether they have ji in them or not. One might observe floating around more ji-nashi flutes w/bad intonation than flutes w/filler. This doesn’t mean that therefore ji-nashi flutes in general have worse intonation than flutes with ji.
This is because it is easier to make a bamboo flute w/out ji than w/ji. Making excellent shakuhachi, with or without ji, is of course another matter.
Consequently there are many flutes w/out ji that have bad intonation. These flutes are frequently, though not always, made by people who do not have much training, experience or skill. So perhaps there are more ji-nashi flutes with questionable intonation because more of this type of flute are made by people without the necessary skills and experience as makers, rather anything innately to do with using or not using ji.
I am blessed with a number of ji-nashi or nearly ji-nashi flutes with good intonation and that can also produce the second and even third octaves easily. Also, I’ve seen many more ji nashi flutes in others’ possession that play much better than my own. Maybe I’m not as blessed as others….
The flute I play the most on right now is one made with ji, though maybe the filler has been kept to a minimum. I don’t really know.