You can do this in the certificate.php file. (pat/to/your/moodle/mod/certificate/type/{type}/certificate.php).
Change this line of code: (line 100)
certificate_print_text($pdf, $x, $y + 70, 'L', 'Times', '', 18, $course->fullname);
To:
certificate_print_text($pdf, $x, $y + 70, 'L', 'Times', '', 18, $course->shortname);
I tested this in Moodle 2.9 and this worked for me.