I agree that this is too low and is a sign of rubber stamp-iness, but what would be the right rejection rate to make you feel more comfortable about the FISA process?
Agencies come to the court with what they think is a rock solid case, so it's not entirely outrageous that the court would have a very high approval rate. See other similar stats like the conviction rate by federal prosecutors (93%+), where they only drag a defendant into court with very good reason.