Security: when you open a communication channel, undesirables can use it too. In particular, if you're using a virtual machine to contain an untrusted operating system or application, the guest additions introduce several risks.
- There is more code in the security containment (the trusted base), so more risk of bugs that could let code inside the virtual machine affect the host.
- Additional features can be used for their intended purpose, but in an unintended manner. For example an application inside the virtual machine can snoop on all clipboard content of the host.