You do not need to initialize your structure at all due to Perl's autovivification: all intermediates are created automatically. The syntax below should work in both versions of Perl you are using.

use strict;
use warnings;

my %exonHash;
my $exonNumber = 1;
my $med = 3;

push @{ $exonHash{ $exonNumber }->[ 2 ] }, $med;
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