Each time you trust a new version of a .dll, it will add its line to the trusted section in the FSX.CFG. It's safe to remove the unused ones (you can simply remove them all, and FSX will again ask to trust the current installed version).
However, the current version of the stand-alone Addon Manager installer and the KDFW installer as well will do this automatically, if you uninstall them and reply Yes to the question "Do you want to remove the Addon Manager?" that is made at the end of the uninstall process.