Other forms of executive privilege that protect autonomy are easier to invoke, and easier to challenge. State secrets privilege cannot be used lightly. It's used all the time now, and there is reason to be suspicious that it is used fraudulently.
The courts really need to figure out a way to in principal allow US citizens bring a case in situations like this. You have to prove now, in essence, that your name is on an invisible piece of paper. I agree that the nomination procedure is extremely sensitive, but I think there is some room on the yes/no presence of someone on the kill list, given other supporting evidence. The danger is that we reveal to someone that we're trying to kill them -- but again, we're talking about a citizen, and if they have supporting evidence and are in court then they already suspect that.
The Constitution describes a separation of powers. The executive has primacy when it comes to waging war. Courts have primacy in protecting the rights of individuals domestically. The Supreme Court has held that U.S. citizens outside the territorial jurisdiction of the U.S. have certain constitutional protections, which can be adjudicated by U.S. courts. That puts those spheres of power into conflict. On one hand, courts generally don't get to second-guess the military's targeting decisions. On the other hand, if a U.S. citizen alleges that the military is targeting strikes in a battlefield in an effort to kill him, that's exactly what the court has to do.
Other developed countries also distinguish executive from judicial power, and domestic from foreign theaters. How they address this tension is illuminating, I think.