If your model is already flat, you don't really need to give it another flat coat. If you have applied weathering powders to the your model, then you would want to give it a flat coat to seal it. Usually this will reduced the effect of the weathering powders. On the other hand, if your weathering effect is caused exclusively by paint, applying a flat coat, shouldn't have much of an effect one way or the other, aside form either making it slightly more glossy or slightly more flat, depending on how flat your original paint is and how flat your clear flat is.
When doing gloss/decal/flat, the net effect should not be too much, although it may even out the colors a bit. When you apply the gloss coat, your colors will deepen and look a lot darker, making you think you screwed up your model. However after applying the decals (and another gloss coat over the decals to really blend them), the flat coat should make your colors come back to more or less what the looked like originally.