You can set security on the active version of a document, or any non-active version of a document, just like you would any other document. The only difference is that since non-active versions are read-only, you may notice that some permissions do not apply, such as Write and File Write (you can turn these permissions on or off and they have no affect, since you cannot edit the version’s properties, nor can you check out the document to edit its attached file). However, other settings such as Change Permissions, Delete, Read, No Access, are valid and will affect the version just like any other document.