Its great that LightSpeed has all the boiler plate for Soft-Deleted entities. However, the major missing link is the ability to Include these Soft-Deleted entities in Query Joins. I have written fantastic Queries with multiple (optional) search criteria (including related tables) that would've been a nightmare to write in SQL. However, this one small gap is extremely frustrating. Specifying IncludeDeleted on the main Query's Entity Type is not enough, we need to carry that forward to Joined tables as well.
My suggestion is to:
Add an extra parameter on the Join creating functions - Join.Inner, Join.Outer, Join.Cross - that specifies whether to IncludeDeleted. So:
public static Join Inner
Status: In current nightly build