When an Admin is in the process of creating an ext. user, the Admin only sees the option to tick/untick the "Publish in Company Directory" for 1) User, 2) Contact phone, 3) Mobile phone; there's no option for "Phone Numbers". The Admin will have to finish creating the user extension then go to Phone System > Phone numbers > All numbers > Search for the TN > Under Company Directory Settings > Publish in Company Directory to "untick" the DID from the Company Directory. This method is tedious especially if there are hundreds of DIDs that need to be excluded from being published in the Company Directory.