Some recommend cutting flashed glass on the clear or non-flashed side. This is based on the idea that the flash is only laminated to the main body of glass. My view is that flashed glass has proved to be very stable over many centuries, and so is firmly a part of the whole sheet.
What is more important is to observe that flashed glass often has a bow. If you place the glass on the bench, you may find that it rocks or sits up from the bench. If you cut the glass on the convex side, that is the side which is not resting on the bench except at the edges, you may find that you break the glass during the scoring, unless you are using the lightest of pressures. It is more certain to get a good break if you score the glass on the concave side - that is where the edges are slightly raised from the bench. So the important element in deciding which side to cut is to score the concave side whether that has the flashed colour or not.
This does not occur with all flashed glasses, and is more important on large sheets than small ones. On the small ones, the curvature is so small as to be immaterial.