No, there is no way to avoid loops when working with cell arrays (including those hidden in cellfun). However, if you are storing things in cell arrays, it probably means your data isn't large enough to make efficiency a very big concern.
If A{1:n} are all same size matrices, it would have served you better to store them as a 3D array,
A3d=cat(3,A{:});
You could then create a similar, zero-padded 3d array by doing,
A3d_=zeros(...);
A3d_(i:j,m:n,:)=A3d;
