The for ... in *.bak command searches only the current directory.

You want instead to use the find command, which searches recursively. This command will locate all zip files starting with a dot at any depth in the current directory (.).

find . -iname '.*.zip'

Removing the leading dot is a bit trickier though. The following seems to work (but may have edge cases, caveat emptor).

for f in $(find -iname '.*.zip'); do f2=$(echo $f | sed -re 's/(.*)/.(.*)/1/2/'); echo $f $f2; done

This will print all the operations it would perform (echo $f $f2), if this list looks right change it to mv $f $f2 and it will do the renames.