Yes some "xbee shields" assume a 5 volt Arduino but probably only to lower the voltage to the 'Bee to 3.3 volts. Digi Xbee radios are powered by 3.3 volts but have 5 volt tolerant data pins so most shields probably do not level shift those.
Some other radios that use the "bee pinout" are 3.3 volt only, like the Sparkfun Wifi module so one has to be careful there.
With the Due, one should look to use the hardware serial lines as there are several to choose from.