I, too, seem to be getting the output I think you want to get from the OPed code (with missing  $ sigil restored):

c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my $line = 'foo';
 my @data = qw(hi ha ho);
 my @site = (9, 8, 7);
 my %lengths;
 ;;
 $lengths{$line} = { x => $site[0],  y => $site[1],  z => \@data };
 dd \%lengths;
 ;;
 for my $coord (keys %lengths) {
   for (@{$lengths{$coord}{z}}) {
     print $_;
     }
   }
"
{ foo => { x => 9, y => 8, z => ["hi", "ha", "ho"] } }

hi
ha
ho
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