The orbiter itself doesn't necessary run Windows 98. The ESA programmers interviewed in the article just mention that the original development environment for the mission software was Windows 98.
OK, but this is much less interesting to discuss than ’was this an official Microsoft update or did they go to the grey market or even P2P’ 🆒🆒The article is frankly nonsense. Mars Express does not run Windows 98, and does not host a single processor capable of running x86 instructions let alone Windows!
Mars Express uses multiple Dynex MA31750 CPUs clustered in pairs onto a CDMUs (Command & Data Management Units), of where there are also a pair (for 4 total CPUs), all running the 1750A instruction set. Mars Express uses an RTOS rather than a regular desktop OS, very likely VxWorks (the project predates ESA's switching of most of their development to RTEMS).
Beat me to it!
There is a joke in here about the desperate search for water too.