> I'm using the Linux command line version.

It is the %q0 option (-%q0) - generally, you can 
quickly find what you want using something 
like 'httrack --quiet --help | grep -i whatyouwant':

Example:
$ httrack --quiet --help | grep -i query

 %q *include query string for local files (useless, 
for information purpose only) (%q0
 don't include) (--include-query-string)
  %Q query string MD5 (128 bits, 32 ascii bytes)
  %q small query string MD5 (16 bits, 4 ascii bytes) (-
-include-query-string)
  %[param] param variable in query string