Alasdair,
We have closed the system OS to ensure stability and system integrity. Win CE is a very stable OS, it's when outside drivers and programs not designed for the device find there way into the system and create vulnerabilities.
It's not recommended to added additional programs and unverified program as we don't support access to the underlying OS. It is only used to run our iFly Software. Many other aviation devices use Win CE in a similar fashion. I hope this helps.