the motors are DC motors of different kinds, but the individual kind is not of interest and doesn't matter.
The H-Bridges I'm currently using are L293/L298 pin compatible but much more powerful.
Currently I'm using on a Mega:
enable-pwm pins (8 Dpins) 2-13
in1/2 pins (16 Dpins) 24-50
IRQ encoder pins (16 Dpins) rest of 24-50
this is all working fine with my 5V Mega board, but for the Due the H-bridges don't work because of 3.3V signal level.
Over and above that, prospectively probably on Tre then indeed there are too few 5V pins left for real-time encoder readings at all (200µs timer-IRQs), and the rest is 3.3V anyway.
So a 3.3V / 5V motor shield (or an external board if not stackable) providing more motor-control-pins by a bus system (e.g., CAN-Bus or I2C) would be appreciated.
The 16 encoder pins can be polled partially independendly from the motor output control pins directly by the Arduino pin headers, if in need, maybe even using analog pins additionally.