As for Windows 2012 and SMB 3.0, encryption is now supported. But disabled by default. You can activate it :
To enable encryption for an individual share, run the following on the server:
Set-SmbShare –Name <sharename> -EncryptData $true
To create a new share with Encryption turned on:
New-SmbShare –Name <sharename> -Path <pathname> –EncryptData $true
To enable encryption for the entire server, run the following on the server:
Set-SmbServerConfiguration –EncryptData $true
Beware that clients not supporting SMB3 (prior to Windows 8) won't be able to connect using this version of the protocol.