tl;dr
If you use DbContext in EF6 this is fixed.
If you're using EF5 (or ObjectContext in EF6) you need to set ObjectContext.ContextOptions.UseCSharpNullComparisonBehavior to true. To do that on DbContext use this:
((IObjectContextAdapter)db).ObjectContext.ContextOptions.UseCSharpNullComparisonBehavior = true;
.
More details
The root cause of this issue is a difference in how the database compares null values and how C# compares null values. Because you write your query in C# you want to use the semantics of C#.
In EF5 we introduced ObjectContext.ContextOptions.UseCSharpNullComparisonBehavior, which allowed you to opt in to using C# semantics instead of database semantics. The default is false (so that existing queries don't magically start returning different results when you upgrade to EF5). But you can set it to true and both your queries will return rows.
If you are using DbContext in EF5 you need to drop down to the ObjectContext to set it:
((IObjectContextAdapter)db).ObjectContext.ContextOptions.UseCSharpNullComparisonBehavior = true;
If you are using EF6, then it's already set to true on DbContext so you are good to go. We decided this causes so much confusion it was worth taking the potential impact on existing queries.