Bigest advantage to the #40L is that it sits lower and will fit better under a traditional magnified scope like a leupold, etc. The disadvantage for most is that when you flip it up, it will default to the small apperature. Most people like to shoot with the large, ghost ring apperature.
The #40 L has a unique style apperature, its not set up like the regular apperatures you are used to seeing. You can get around it defaulting to the small apperature by removing the small peep hole. Once you do this, all you will have is the large apperature and the #40L will default to that from then on. But thats all you will have is the large, no small.
In my opinion, getting either the #40 or #40a is a better choice for something like a EoTech. The only reason to really get a #40L in my view, is if you need to fit it under something like a scope. I have all three and like all three. Generally, though, I like the #40 best.