You're right. They weren't Nilotes but something similar (proto Nilotes acc to some on here). These ancestors are extinct.
Nilotes have also changed a lot over time and mixed in with other people. You can't really compare a modern population with an ancient extinct one.
@Luna
Haplogroups are ancient, proto Nilotes would have had the same signature DNA markers that are currently not found in any Somali populations above noise level. Same goes for Cushites generally.