Advantages and disadvantages of each method in my opinion:

Method 1
+ Completely specifies each row/column
- Difficult to remember the 6-character legend

Method 2
+ Simplified version of Method 1
- L appears twice as often as I, making it somewhat guessable

Method 3
+ More consistent with other shading answer keys
- 1 and 2 can't quite differentiate I's and L's

Method 4
+ Centers are not easy to guess
- Probably difficult to notice

I myself seem to prefer Method 3 slightly, with Method 2 coming second.