For what it's worth, I'm running Firefox 3.5.7 and it opens .shtml as if it was
.html.  So unless I'm misunderstanding the problem, maybe it's your browser.

Nonetheless, as I understand it, the MIME type "assume" (aka %A) option is
supposed to be able to do this for you.  I've had problems (yet to be posted)
with this, but it might be worth a try for you.

Either, 1. go to WinHTTrack's MIME Types tab and enter shtml under File types
and text/html under MIME identity,
Or, 2. add
--assume shtml=text/html
in the scan rules tab

I should note that this didn't work for me when I tested it for you before
posting.  But I'd like to know if it works for you or not :)