She can delete all the text messages from the phone.
Where you were looking would show any text messages that were sent and received. There’s nothing she can do to edit that information.
Don’t worry about or suspect those with the missing phone numbers. So far in our investigation of why they are appearing that way, we beleive they are not text messages, but other things happening on the service line, like messages from short codes and transfers to voicemail.
She might also be using some sort of messaging app that doesn’t use the phone service - like Facebook messenger, Snapchat, or Whatsapp. Those messages would not be logged in the account call and text history.
You may want to look into an app like https://www.qustodio.com/en/ if you need some help as she learns to explore her boundaries.