Did some more digging and found the following solution

var selfJoin = 
    from child in Context.GlobalDocumentClassification
    from parent in Context.GlobalDocumentClassification
    select new { child, parent };

var query = from item in selfJoin
    where item.child.HierarchyId.IsDescendantOf(item.parent.HierarchyId) &&
        EF.Constant(ids).Contains(item.parent.Id)
    select item.child.Id;

This produces SQL-Server cross join query and allows for the use of IsDescendantOf() in the queries where clause.