Keep in mind, no matter where you get your training, YOU are responsible for the quality and completeness of your education/training.
ATP's system, in many ways, expects this from you. You're expected to do a large amount of self study. Of course, they'll provide lessons on specific topics and go over areas that need improvement or where there is confusion, but for the most part, you're not going to get hours and hours of ground school on a given topic.
No matter what field (medicine, computers, law, aviation) or where you study (Harvard, community college, ATP), no one is going to take more interest in your education than you are.
If you are expecting to be "spoon-fed" and rely solely on what you are told or experience in the program, then you are definately going to exit the program with less understanding and experience than you would have if you had taken full advantage of the resources available to you.
Therefore, if you feel that you do not have a firm grasp of a specific topic, it is incumbent on you to ask and get the answers and/or practice. NDBs and GPS-less operation are definately two areas where questions and practice could be very helpful.
But you, as the student are responsible for acquiring that extra experience. As for those who would be totally lost without the GPS, that's their loss and hopfully they'll never have to encounter an aircraft or situation where that is not available to them.
As for me, I did acquire the knowledge and understanding to safely operate with the ADF and without the GPS (and a healthy respect for how powerful the Garmin 430 really is)--but I did have to consider the possibility, ask questions and get practice to gain that understanding.
Always be a student of your profession. The learning never stops.
Just my $0.02.
Jeremy