Вы получаете меньше строк, потому что вы используете inner join вместо left join.Попробуйте что-то вроде этого:
var result= from table1 in dbo.Table1
from table2 in dbo.Table2
.Where(i=>i.Id == table1.Id)
.DefaultIfEmpty();
или вы можете посмотреть, как Выполнить левые внешние объединения
Person magnus = new Person { FirstName = "Magnus", LastName = "Hedlund" };
Person terry = new Person { FirstName = "Terry", LastName = "Adams" };
Person charlotte = new Person { FirstName = "Charlotte", LastName = "Weiss" };
Person arlene = new Person { FirstName = "Arlene", LastName = "Huff" };
Pet barley = new Pet { Name = "Barley", Owner = terry };
Pet boots = new Pet { Name = "Boots", Owner = terry };
Pet whiskers = new Pet { Name = "Whiskers", Owner = charlotte };
Pet bluemoon = new Pet { Name = "Blue Moon", Owner = terry };
Pet daisy = new Pet { Name = "Daisy", Owner = magnus };
// Create two lists.
List<Person> people = new List<Person> { magnus, terry, charlotte, arlene };
List<Pet> pets = new List<Pet> { barley, boots, whiskers, bluemoon, daisy };
var query = from person in people
join pet in pets on person equals pet.Owner into gj
from subpet in gj.DefaultIfEmpty()
select new { person.FirstName, PetName = subpet?.Name ?? String.Empty };