Learn English – Questions without a subject

It is true that in general in English, 'some' is replaced by 'any' in negative and interrogative contexts. But it is not as simple as that: 'Some' can be used in interrogative contexts, and is then 'marked' as linguists say: choosing it rather than the default conveys some meaning.

I would disagree with kajaco about just what nuance is conveyed: to me the choice of 'some' rather than 'any' is meant to exclude 'all'. So

Why are any organisations using X

may be appropriate even if all organisation are doing so (though the question is perhaps a little unlikely if everybody is doing so); whereas

Why are some organisations using X

implies "and others are not".

Negative questions are used when the person who asks expects a positive answer, no matter what else might be implied. There is no question of frequency of use; when the speaker wants to express an amount of certainty for the answer, a negative question will be used.