Unless your goal is to produce an actual scale model, the choice of the initial size for the main building walls is a practical one. You are constrained by the size of cardstock your printer will print but also by how you plan to display your creation. If you plan to put the model on a mantle, for instance, the base must fit there.
Another consideration is the person who will build the model. If you are designing for use by a small child, for example, the size of the smallest elements must be large enough for inexperienced hands to manipulate.
Keep a ruler beside your design station as a thinking tool. After you make a preliminary decision on the size of the footprint of your model, measure it out on your desk and consider whether it looks too large or small for ease of construction. Once you make the first piece, that sets the scale for the entire model, so be sure you are comfortable with that decision.