To add to the other answers, a Yubikey generally cannot emulate a different device other than a HID, such as a mass storage device as you suggested. Many large organizations deploy policies that prevent the use of removable mass storage devices by users in order to help thwart data loss. Those policies are intended to prevent a malicious user (or Bad USB cable) from downloading sensitive files locally. They also protect against users plugging in “found USB keys” that upload malware. 

When such a policy is enabled, the OS will see that a new USB device is a mass storage device and will refuse to mount it. A Yubikey would be inert if it was emulating a thumb drive. 

But unknown HID devices (like new keyboards) are almost always allowed because of accessibility issues. For example, if a person requires a specialized large button keyboard, a US employer is required by the ADA to permit them to use it so they can do their job.