I find sentences 1 & 2 awkward (at best) because of the positioning of "not":
- Not only have these conditions been not prepared in developed countries, but developing countries also have not accepted them.
- Not only have not these conditions been prepared in developed countries, but also have developing countries not accepted them.
As @EdwinAshworth has commented, sentence 3 has a different meaning because the other two sentences refer to acceptance by developing countries, whereas the last sentence refers (implicitly) to preparation by developing countries:
3- Not only have these conditions not been prepared in developed countries, but (also) in developing countries.
Although I'm not 100% certain what you're trying to say, my suggestion of rewording while retaining your words as closely as possible, would be to adopt the first part of your sentence 3, with a modified version of the last part of your sentence 1:
Not only have these conditions not been prepared in developed countries, but neither have developing countries accepted them.
Not only have these conditions not been prepared in developed countries, but neither have they been accepted by developing countries.
Of those, I prefer the latter because the second part more closely reflects the first part:
Not only have these conditions not been prepared in developed countries, but neither have [the conditions] been accepted by developing countries.