The number of windows, as well as their sizing and placement, depends on your orientation, view, desire for ventilation, and needs for daylight and solar gain. Orienting more of your windows towards the south side of your shop and placing them high enough that they are shaded by the eaves in summer, but allow lower-angle winter light to come in, will increase your ability to get free light and heat from the sun. If your goal is to take advantage of passive solar opportunities, make sure that you carefully research the type of glass that is in your windows and look for something with a high solar heat gain coefficient. Higher windows generally allow for benches and tools beneath them, and relatively windowless north walls may be a place to arrange wood storage or mechanicals.
Let’s be clear about one thing: No workshop is perfect for everyone. If there were, I could simply give you a precise plan to follow with clear dimensions. Every person who comes to the hobby, avocation, or profession of woodworking has his own particular collection of tools and his own peculiar work style, skills, and desires for the kind of woodworking he wants to do that gives him a unique approach as to how he will lay out a shop: where the tools should go, where lumber and supplies are stored, and how much bench area he needs.