In practical terms, the two words are somewhat similar.
However, they do come from different roots and the verb "certificate" involves the furnishing with, and/or authorising by, a bit of paper called a certificate. "Certify" has a number of meanings, including one similar to "certificate", but generally involves more the intent of formal attestation rather than the formal issue of a bit of paper to frame and put on the wall.
It has been traditional in airworthiness circles (particularly) for far longer than I have been in that game to use the verb "certificate".
Now, if you don't like that, then feel free to use "certify" - it doesn't really matter and, ultimately, becomes a point of preferred style. However, be prepared to continue seeing the other, probably somewhat more appropriate term, used by the trade.