I will answer my own question looking at some test that I have made:
As far as I check, it is possible to use as the CNN input a matrix consisting in purelly negative number, using .mat files as database elements, and it works pretty well. However, when use it, it is highly recommended not to use the "ReLU Layer", due to the fact that if it is used, most of the Matrix will become 0.
I hope in any update soon Matlab implement another kind of activation layer, such as PReLU or another that dont send al the negative matrix to 0, and also build a dtabase not using only the "imagedatastore" function =).
Hope it helps to any body want to use the CNN toolbox for processing not images but anything else.