What you're doing is called "clubbing somebody to death with a loaded Uzi": instead of if iterating over all hash keys and looking op if one is equal to another key, you can simply look up the second key:

my $key = 'res.ldlibrarypath';
for my $hashref($HR_wnt,$HR_unx,$HR_component) {
    if (exists $hashref->{$key} && $hashref->{$key} =~ m{/}) {
         $hashref->{$key} =~ s{/opt/app/$target.*?:}{}
    }
}
[download]

Your hash is updated after that substitution if the regex matched, so I don't quite understand what your question is about.