Maybe you want an array(ref) of hash refs so you can use the hash key as the column name? Probably not as memory efficient as an AoA depending on empty columns.

my $ary = [
    { c1 => 1, c3 => 3 },
    { c2 => 2, c3 => 3, c4 => 4 },
    { c5 => 5 },
];

my @cols = qw( c1 c2 c3 c4 c5 );

# to set a vaulue in a col that may or may not exist....
$ary->[0]->{c2} = 2;

# print out as a table
print join "  ", @cols, "\n";
for my $ref( @$ary) {
    print join "   ", (map{ defined $ref->{$_}? $ref->{$_} : '~' }@col
+s), "\n";
}

__DATA__
c1  c2  c3  c4  c5  
1   2   3   ~   ~   
~   2   3   4   ~   
~   ~   ~   ~   5
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