Some of the flash processes for dense flash storage have retention times of just a year or two, and need regular automated refresh. Store them too long in the draw and they are dead. They are starting to look like slow DRAMs These are not the processes used for MCUs. People expect a sense of permanence from their MCUs.
Flash embedded into a microcontroller would normally be NOR flash to provide random access but I am sure there is pressure to make it as dense as possible.
I have run across a few embedded designs now where the firmware for the microcontroller is stored in external NAND Flash and read into RAM for execution. If they use cheap high density NAND Flash, at least they will not have to worry about tin whiskers from lead free solder causing a failure.
Do the various NAND Flash memories with embedded controllers refresh their contents while powered?
Update:
The similar Cortex M3 based microcontrollers from ST and Analog Devices specify a 10 year retention at 105C and 85C respectively so I think the lack of a temperature in the specification is just an oversight on Atmel's part and they may by 100 years at 25C.