Hi
My apologies for the really long delay in responding to this, unavoidable I'm afraid.
However, I think I have solved the issue, by changing two files, not just the one you quoted. In both the files below I changed the href which was originally "index.php" to "/". I hope this is correct and will not cause any issues. The logo is now no longer showing /index.php when selected.
The files I edited are:
/public_html/plugins/system/t4/themes/base/html/layouts/t4/element/logo.php
/public_html/plugins/system/t4/layouts/t4/element/logo.php
Thank you for your help on this. Much appreciated.