Settlements with confidentiality/nondisclosure clauses generally come about because one side has decided that it is more expedient to settle than to pay the costs of a dragged-out court case. With the government you can be sure it was not because they were worried about the costs involved.
Those whose rights were violated often settle because they are under the mistaken impression that doing so will set some sort of precedent that will keep the government from doing the same thing to anybody else. The worst-case scenario, IMNSHO, is the non-consent decree, AKA "I did not do it and I promise never to do it again."
Heck, if I could get a court ruling that sets precedent in the jurisdiction, I'd gladly accept $1.00 (One Dollar) plus costs. It's not the money, which is to compensate me for the violation of my rights and/or to punish the person/agency that violated those rights. It's the fact that the person and/or the agency they work for, as well as all other similar agencies within the jurisdiction of the court deciding the caseare now under notice that the action violated a right. That way not only does the plaintiff win but everybody else wins as well.
Without the court ruling (as happens with a settlement, which means the parties have agreed to end the case before the court rules on it) the offending individual/agency can commit the same act against another person and claim they were unaware it violated any right.
All that is difficult to do if you are paying your own legal costs. It can get downright difficult to get someone else to cover your costs when the odds are not 100% in your favor. If anybody can point me to a case which was an absolute slam-dunk from the beginning, I'd like to study it.