You have to write the version number into the web deployment project file itself. This NAnt task should do it:
<target name="setAssemblyVersion" description="Increments/Sets the AssemblyVersion value" depends="getAssemblyVersion">
<foreach item="File" property="filename">
<in>
<items>
<include name="**/*.wdproj"></include>
</items>
</in>
<do>
<script language="C#">
<code>
<![CDATA[
public static void ScriptMain(Project project) {
string contents = "";
StreamReader reader = new StreamReader(project.Properties["filename"]);
contents = reader.ReadToEnd();
reader.Close();
string replacement = string.Format(
"<Value>{0}.{1}.{2}.{3}</Value>",
project.Properties["build.major"],
project.Properties["build.minor"],
project.Properties["build.build"],
project.Properties["svn.revision"]
);
string newText = Regex.Replace(contents, @"<Value>([0-9]+\.){3}[0-9]+</Value>", replacement);
StreamWriter writer = new StreamWriter(project.Properties["filename"], false, Encoding.UTF8);
writer.Write(newText);
writer.Close();
}
]]>
</code>
</script>
</do>
</foreach>
</target>
I'm guessing your NAnt property names...