from t in Assemblies
means that t is an assembly.
You should try from t in Application.Types
:
// <Name>Display relationships between two types</Name>
from t in Application.Types
where t.DepthOfIsUsedBy("Company.Project.NamespaceA") >=0 &&
t.DepthOfIsUsing("Company.Project.NamespaceZ") >=0
select new { t, t.NbLinesOfCode}