The Silverfish template does support the EZ-Pages links and the code that generates them is working as you see them when you switch back tot he Classic template. So the problem lies somewhere in your specific version of the Silverfish template.

Since say you've overridden every Zen Cart file (which is a very odd thing to do) and it's not clear where you got to files to do so from, and you haven't answered the question about what files your then "reuploaded", it's difficult to advise further. But you might want to check your tpl_header.php file if you made any changes to it, to ensure that you haven't accidentally remove its inclusion (towards the bottom of the file and clearly marked if it's there).