File1
Name: main.pl
Content: print "hi\n"

File2
Name linkdir/main.pl
Content: symlink to File1

Run:
$ perl -MDevel::Cover main.pl
Devel::Cover 0.76: Collecting coverage data for branch, condition, statement, subroutine and time.
    Pod coverage is unavailable.  Please install Pod::Coverage from CPAN.
Selecting packages matching:
Ignoring packages matching:
    /Devel/Cover[./]
Ignoring packages in:
    .
    /usr/lib/perl5/5.10.0
    /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/vendor_perl/5.10.0
    /usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi
    /usr/lib64/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi
    /usr/local/lib64/perl5/site_perl/5.10.0/x86_64-linux-thread-multi
hi
Devel::Cover: Writing coverage database to /path/to/cover_db/runs/1311608639.28154
----------------------------------- ------ ------ ------ ------ ------ ------
File                                  stmt   bran   cond    sub   time  total
----------------------------------- ------ ------ ------ ------ ------ ------
main.pl                              100.0    n/a    n/a    n/a    n/a  100.0
Total                                100.0    0.0    0.0    0.0    n/a  100.0
----------------------------------- ------ ------ ------ ------ ------ ------


$ perl -MDevel::Cover linkdir/main.pl
Devel::Cover 0.76: Collecting coverage data for branch, condition, statement, subroutine and time.
    Pod coverage is unavailable.  Please install Pod::Coverage from CPAN.
Selecting packages matching:
Ignoring packages matching:
    /Devel/Cover[./]
Ignoring packages in:
    .
    /usr/lib/perl5/5.10.0
    /usr/lib/perl5/vendor_perl
    /usr/lib/perl5/vendor_perl/5.10.0
    /usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi
    /usr/lib64/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi
    /usr/local/lib64/perl5/site_perl/5.10.0/x86_64-linux-thread-multi
hi
Devel::Cover: Writing coverage database to /path/to/cover_db/runs/1311608812.28180
----------------------------------- ------ ------ ------ ------ ------ ------
File                                  stmt   bran   cond    sub   time  total
----------------------------------- ------ ------ ------ ------ ------ ------
linkdir/main.pl                        n/a    n/a    n/a    n/a    n/a    n/a
Total                                  0.0    0.0    0.0    0.0    n/a    0.0
----------------------------------- ------ ------ ------ ------ ------ ------