I don't know this for sure, but I suspect that if you contacted JSTOR from a low income country they may give a better deal.
BTW, if you really do need JSTOR, it's not hard to find a library card number from a US library and use that for access anywhere. (Well, I don't know JSTOR specifically, but all the other databases I've used from my library are available to me at home after I put in my library card number.)
Their price schedule divides "Public Library – Small" into "US", "Canada", and "Rest of the World". It's possible that someone phoning them up from Senegal or Paraguay would be able to negotiate a lower price, but it's not as if their existing price list doesn't recognize the existence of different countries. (Still, lumping Switzerland and Malawi into the same category might not represent a deep level of consideration of the issues.)
For what it's worth, I was using their web site from my house here in Argentina, which is usually classified as a "middle-income country," but where you can hire a full-time employee illegally for US$4000 per year.
BTW, if you really do need JSTOR, it's not hard to find a library card number from a US library and use that for access anywhere. (Well, I don't know JSTOR specifically, but all the other databases I've used from my library are available to me at home after I put in my library card number.)