All right, here I am again.
IOBit's Smart Defrag finally did it: about 8hrs of analysis, and then about 18hrs of defragmentation, and the disk was OK again. And to think that HTTrack created this mess in only a few days..
So Kudo's to IOBit for really fast defragmenting, and to Auslogics for really fast analysis (if no more than 2000 fragmented files are created per day, their screensaver is great: give it five minutes or more and it will do useful work in that time).
And to MyDefrag, of course, for giving really fine-grained control over the disk layout!
Anybody for combining these three properties into a single program?