I would not use either of the first two methods, because they are an easy way to get latent, almost undetectable errors in your data. You might assume that your data is perfect and write your code accordingly, but that is not a robust approach. Consider what would happen if one of the files is missing any of those variables: the variable value from the previous loop iteration would get used without any warning whatsoever. No doubt you will say "but my data are perfect and are not missing anything..." sure, sure.
Much more robust (and more efficient) is to ensure that every file imports the required data:
S = load(...);
and the simply access the fields of the structure S:
S.var1
S.var2
...
This also answers your next question:
"is there a way to load these files altogether at once even though they are built the same way"
Of course, this is MATLAB, so just use a structure array! If every mat file contains exactly the same variable names (as they should) then your task is easy, you can just do this:
S(j,k) = load(...)
If the mat files contain different variable names then go and yell at the person who created them.
"is there a way to create dynamic names for variables ...so I can load more than 1 file at a time ?"
Importing multiple files can be done simply and efficiently using indexing into one array, there is absolutely no need to use ugly, slow, inefficient, complex, overused-by-beginners dynamic variable names.
