> folder/file0df0.html
> 
> I am using %h%p/%n.%t in the options and selecting
> Hide Query Strings, but I continue to get the funny
> filenames.

Folder/file?ID=1 folder/file?ID=2 and folder/file are all different files, so
httrack has to make them unique on disk:
folder/file0df0.html

The Hide Query only removes the ?ID=2 from the links:
url="folder/file0df0.html?ID=2"