Not sure exactly what wasn't working for you, but the following edit works per your specification.
#!/usr/bin/perl
my $skip_users = &get_data;
&print_data;
sub get_data
{
my %skip_users;
my $skip_id = 'fred';
my $value = 'ethel';
#build a hoh with userid and value.
$skip_users{$skip_id}{$value}++;
return(\%skip_users);
}
sub print_data
{
my %hoh = %$skip_users;
my $user = 'fred';
my $command = 'thel';
if ((exists $hoh{$user}) && (exists $hoh{$user}{$command})) {
print "yep\n";
} else {
print "nope\n";
}
}