as of 5 minutes ago, NWA's website still claims that KQ flights do not earn EQMs.
This is frustrating to me as well, as I make about 6-7 trips to Africa a year. I've asked several people at the plat desk about this and have gotten no good answer.
You might be better off flying KLM from Amsterdam and then taking KQ for short hops from Kenya, if KLM does not fly directly to where you want to go