I think the age-old saying "if it ain't broke, don't fix it" applies to this scenario. Chances are the hardware in the Jornada you have was designed to run on the 2000 version. If it is possible, there may be compatibility issues between the hardware and operating system in the 2003 version. Just imagine installing Windows XP on a 4-5 year old computer.
Heck, there's software only a year or two old that's not compatible with Service Pack 2.