Yes I have this problem to, its been documented for years that HTTrack wont
download this or anything else that doesn't have an HREF.

I have a site with thousands of images...like this, I mean thousands and get
everything but these pictures I need.

I'm writing some python code to seek out those javascript links, massage the
link there, like it may need some front path information on it, then python
downloads the link, saves it, renames the link in the mirrored site to where I
saved it. But I'm still in process.

For instance, your trouble  line is:
< a href="#" onclick="popupCenter('/apex/PDFfile?id=12345', 'PDF File');

if you extract the /apex/PDFfile?id=12345 from the line, then put the webiste
<http://teammarinedemo.force.com> infront of it such that you build the link
<http://teammarinedemo.force.com/apex/PDFfile?id=12345> you should be able to
enter that in another browser window and see the file come up or in my case
the picture comes up, I did it as a test to prove I could get at it. IF the
site requires a login in ensure you are logged in before doing this.

Give it a try to see if that gets your image, then write the code, it is
complicated but the only way I know of.