There are two different licenses involved here: Server Licenses and CALs (Client Access Licenses).
A Windows DC needs a licensed copy of the Windows 2008 R2 operating system, the server license. This requirement is unaffected by other license requirements in your network. The Samba DC does not require such a license, as it is a GPL implementation of the SMB/CIFS and AD protocols.
In addition, a client accessing a server needs a CAL
. There was a time when a CAL was only needed for clients specifically accessing file or print services (up to and including Windows 2000, I believe), but the current licensing rules demand that every connection to a Windows domain needs a CAL (tied to either the device or the account of the logged-in user). You should definitely read the fine print on your license agreement to verify this.
Since CALs are tied to either a device or a user account, one would think that simply adding another server (Windows or Samba) to the network should not affect the required number of CALs. But here's where it gets slightly murky: since a Samba DC is a domain member accessing AD on the Windows server for replication and authentication purposes, one might argue that each Samba server will need a CAL to join a domain with Windows DCs.
It all depends on how Microsoft defines a "client", but I know for a fact that joining a Windows server (DC or member server) to a SBS 2003 domain consumes a CAL. This could of course be specific to the SBS license model. You will need to check the fine print on your license agreement for the specifics.
Of course, once all Windows DCs have been eliminated from the domain, no CALs are required to join the domain. CALs may still be necessary to access services on member servers running Windows.
In my opinion, the only way to be reasonably certain you're in the clear with regards to licensing, is to get a written statement from a Microsoft representative.