Atmel have confirmed the SAM3UE used on the Arduno Due does only have one quadrature decoder.
IMHO this is not a big issue for most users.
By comparison the STM32F103xB on Maple and Maple Mini has 4 timers each of which implements a quadrature decoder. Maple Native and Maple RET6 have 6 timers which implement quadrature decoders.
For mobile robots, for example Micromouse, which often have (at least) two independently driven wheels, only one quadrature decoder is a bigger issue. Keeping track of position (odometry), and speed is crucial for many mobile robots. Odometry is essential for Micromouse maze solving, and also gives a big advantage for line following robots which can use odometry to 'learn' a track. Some mouse builders use stepper motors which remove the need for encoders, but the fastest, most agile or lowest cost mice use DC motors which require two decoders. Even simple 'toy' robots which try to follow a pre-defined route would be easier to build with a quadrature decoder for each independently driven wheel. Something like a robot Scalextric car are likely okay as they have only one driven axle.
It is practical to do quadrature decoding in software, but folks I talk to, who compete nationally and internationally, say there are often problems debugging the real-time code; errors can result in the robot crashing. Also high-performance miniature DC motors from Faulhaber and Maxon Motors with built in hall-effect encoders can generate 100,000 interrupts per second and more. So catching the quadrature interrupts, and not interfering with another real-time subsystem are hard problems to debug.
Summary: quadrature decoders are an important resource to some classes of use, but irrelevant to most. I'll certainly mention this when people ask for my advice.
