The page you note above has nothing to do with the "read" permissions of the
directory or of the files.  It simply means that there is no "index.htm,"
"default.htm" or other file name set as the index page for that directory by
the web server.  

A webmaster can set a web server to automatically load a file if no file name
is provided in the address bar.  So, if the webmaster set "index.html" as the
default page for <http://some.server.org/>, then, if you type that address, you
will see <http://some.server.org/index.html>.  If the webmaster sets the web
server to show no default file, then you will see the page you noted above. 
This is true for any subdirectories of the web server, as well as the web
"root" directory.  Specific files which are explicitly named in the
location/address bar and have permissions set to "read" by all will display in
the browser - whether IE or HTTracker.

I don't believe that HTTracker downloads directories, though, admittedly, I
have not read the code.  I believe it simply looks at the links on a starting
page and downloads the files specifically named in the links (and javascript,
flash and links other than http may not count!).  If you specify a level
deeper than "1" it may look at the links in the second set of html files and
download the files it finds there, too - and so on, until your level
specification is fulfilled.