That’s an interesting topic for discussion: does an organization serving the public have a right to limit who it serves. I think the answer is yes, but but it must be based on fair criteria.
A bikur cholim organization will often allocate funds towards local residents much sooner than to other patients requiring aid. They may even have specific types of expenses which they cover, but won’t cover other necessary expenses – not because they aren’t needed, just because limited resources force them to limit their operations. There are some specialty tzeddakos which discriminate in this way. I know of several; some examples are: an organization which covers cleaning help when parents are incapacitated, one which provides linen for needy chasanim and kallahs, one which pays for the jewelry, one which helps with gowns, etc.
As long as the Sefardim and Ashkenazim are considered to have, at least to some extent, different shidduchim pools, it’s fair for one to limit its activities to one or the other.
OTgeneration of the tzeddakos I mentioned would do such a thing, that would be wrong. If a hachansas kallah fund would only give to needy Ashkenazic kallos, or a bikur cholim would only cover expenses for Sefardic patients, my sensitivities would be offended, because for those needs, cultural differences are not a fair criterion.
The reason it’s changing shidduchim-wise, is because the cultural differences are becoming smaller with each subsequent generation, and I don’t think the difference in minhagim is enough of a factor itself to keep the shidduchim pools seperate.