Hello,
For any activities to be able to do a 1.9 -> 2.1 restore, it must contain some code. The certificate module don't have this code and to my best knowledge nobody has tried to write such code.
So currently it is not possible to restore a 1.9 certificate activity in a 2.1 course.
But don't be confused, if you upgrade a Moodle 1.9 website to Moodle 2.1.x the certificates activities are upgraded (because the code used is not the same that during a 1.9 backup restore), even if there are some troubles (for instances conditional certificates, but I think the latest git version from Mark Nelson has make progress in this area) and sometimes upgraded certificates need to be edited.
Hint : To see if a contributed module named "mymodule" is able to do a 1.9 backup restore, look to see if there is a mod/mymodule/backup/moodle1/lib.php file. If there is none, the module is not able to restore a 1.9 backup.