Mars Express will be getting one, however. There's no way they could be installing Win11 on that thing. My guess would be some form of Linux as you can find versions as small as 800 kilobite out there. That would be small enough for it to be installed on the hardware they have, then wipe '98, install the rest of the stuff they need that they couldn't include in the kernel, and Bob's your space probe!
Doesn't sound like the probe itself was using Windows 98, just that the software it is running was written on Windows 98.