First thing: a matrix of matrices does not exist mathematically, so what you're asking is an impossibility. In matlab, you can store matrices in a cell array. cell arrays are not matrices and work differently so may not be what you want. For example you can't perform mathematical operations on a cell array.
Second thing: Numbered variables are always a bad idea and will greatly complicate your code. You're embedding an index in the variable name which is problematic. Instead you should be using a cell array or a 2D matrix to store your vectors. Either way, you then use standard matlab indexing to refer to each vector.
I would recommend you store your X vectors as rows of a matrix:
X = [1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16];
X(1, :) is your original X1, etc.
With that storage, what you want can be done easily without a loop. As said it can't be stored as a 2D matrix. I'd recommend a 3D matrix instead
%Better X for demo
X = [1 2 3 4 5; ... x1
3 5 7 9 11; ... x2
2 4 6 8 10; ... x3
3 9 12 15 18]; % x4
minx = min(X, [], 2); %min of each vector
maxx = max(X, [], 2); %max of each vector
result = X >= reshape(minx, 1, 1, []) & X <= reshape(maxx, 1, 1, [])
result is a numvector x numcolumn x numvector matrix, where result(r, :, p) is the comparison of X(r, :) with X(p, :).
