Problem: Definition queries and definition selection sets are ignored by joins in ArcMap
Definition queries and selection sets defined on the join layer are ignored by the join.
The table underlying the join layer is used to create a join. This table has no knowledge of settings made on the join layer.
Solution or Workaround
Re-create the definition query or the definition selection set after the join.
Spatial joins respect the definition queries and the definition selection of both the join and target layers.