No, such programming does not necessarily increase the runtime. It can be a nice and efficient structure to represent the data. Even if it runs some seconds slower, a clear data representation can save weeks of debugging.
A non-scalar struct is something like this:
S(1,1).a = 1;
S(2,1).a = 2;
S(1,2).a = 3;
S(2,2).a = 4;
Now you have a [2x2] struct with the field 'a'. You cannot save this using the '-struct' flag, but by:
save('filename.mat', 'S');
