copying certs in /config/filestore/files_d/Common_d/certificate_d/

You have to load them in order for them to appear. The files are referenced via the config file. It's not a dynamic check of the FS. I would recommend copying them to a temp dir (keys to /tmp/keys/* and certs to /tmp/certs/*) then you could write a quick script to reference all the objects for loading.

install sys crypto key object_name from-local-file /path/to/keyfile
install sys crypto cert object_name from-local-file /path/to/certfile

from-url is also an option, if you key your keys/certs somewhere your BigIP has access too.