I'm pleased to note that the
link in the OP still works!

Meanwhile, in more recent news ... it has been
reported that the survey ship HMS
Enterprise uses certain systems that rely on Win ME.
So what, says I ... if it works, best leave it alone.

But I agree that
this may be the real (and interesting) reason:-
I strongly suspect the reason for ME was the highly specialist kit that is attached to the systems. The ability to write to memory-mapped IO from user-space used to be a convenient shortcut for developers - avoiding the need to write device drivers (or possibly having to write them in order to port to a newer version of Windows). ME was the last version of Windows where this was possible.
Meanwhile, here's another "so what"! ...
The next time you go into a Post Office and see them using the touch screen behind the counter be advised that under the counter is a Pentium 4 with 256Mb of memory running NT4...