Like you said in your title, fgetcsv is the way to go. It's pretty darn easy to use.

$file = fopen('myCSVFile.csv', 'r');
while (($line = fgetcsv($file)) !== FALSE) {
  //$line is an array of the csv elements
  print_r($line);
}
fclose($file);

You'll want to put more error checking in there in case fopen() fails, but this works to read a CSV file line by line and parse the line into an array.

Use the file() function to read a file into an array. Each line will become an array element.

$codes = file("codes.csv", FILE_IGNORE_NEW_LINES);
if (!in_array($posted_value, $codes)) {
    ...
}

However, searching an array with 80K elements will be slow. If you're doing this repeatedly in the same script, it would be a good idea to hash them, by converting it to an associative array:

$codes = array_flip(file("codes.csv", FILE_IGNORE_NEW_LINES));
if (!isset($codes[$posted_value])) {
    ...
}

The full code should be:

add_filter('frm_validate_field_entry', 'my_custom_validation', 10, 3);
function my_custom_validation($errors, $posted_field, $posted_value){
    if($posted_field->id == 9){ //change 25 to the ID of the field to   validate
        static $codes;
        if (!$codes) {
            $codes = array_flip(file("codes.csv", FILE_IGNORE_NEW_LINES));
        }
        if (!isset($codes[$posted_value])){  //change 001 and 002 to your allowed values
        //if it doesn't match up, add an error:
            $errors['field'. $posted_field->id] = 'Deze code is al een keer gebruikt  of bestaat niet.';
        }
    }
    return $errors;
}

Look into fgetcsv()

<?php

    $handle = fopen("test.csv", "r");
    $result = Array();
    fgetcsv($handle); //Removes the first line of headings in the csv
    while($data = fgetcsv($handle)) {
        $result[$data[0]] = $data[1];
    }
    print_r($result); //the result
?>