I suspect based on
https://github.com/certbot/certbot/blob/master/certbot/main.py#L224
that my guess is right and specifying --duplicate will entirely avoid calling cert_manager.find_duplicative_certs().
@Hoststar, it might not be the best solution, but could you try adding --duplicate to your Certbot command line for a new cert issuance and see if it happens much faster? (The only drawback in this case is that if you do request a certificate that duplicates one that you already have, it will save a duplicative cert instead of updating the old one. --duplicate effectively means "I know that I (might) already have such a cert, but I still want a new one no matter what". So you would probably want to check and take care of that case in some other way.)