The CIA's do leave some traces. When installed they place a permanent entry in your ticket.db file. When you visit the the eShop page of a game you installed the CIA for, the eShop will offer to let you re-download the title. While FBI can remove installed tickets it doesn't not remove the entry from your ticket.db. Your ticket.db also survives factory resets and carries over with system transfers. The only way to "clean" it is to restore a backup you have from before you installed any CIA's. This included Homebrew CIA's.