You can do it right here:

while (my $line = <IN>) {
    #next unless $line =~ m{^(\S+) (\d+) (.*)};
    next unless $line =~ m{^(\S+) NA(\d+) (.*)};
    # Now 'NA' is not captured.
    my ($site, $userID, $data, $data2) = ($1, $2, $3, $4);
    
    $user{$userID}{$site} = $data, $data2;
}
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Coupl'a notes:
$4 is never populated - you only have 3 sets of captureing paran's, so $data2 is empty and meaningless
This regex should've failed all together because 'NA1234' doesn't pass (\d+) in your regex.