This one is more of a personal interpretation, because the use of hover is (as far as I know) never discussed in the MacOS version of their Human Interface Guidelines. I think it's because Apple's philosophy is based on a clear and contrasting use of color and states. A hover effect is a bit of an in-between of an active and inactive state. It's a glimpse of what will happen if you click. Since most of Apple's guidelines are app specific, perhaps they are using the same logic of not using hover states for their entire design library.
macOS is designed to keep the current task clear and in focus. Visual contrast, translucency, and a large drop shadow make it easy to differentiate the active window from inactive windows. Throughout the system, adornments are subtle and appropriate. Interfaces defer to content and related controls.
Hover states would detract from that clean interface. Instead the pressed state has more prevalence in their designs, which makes sense since it's what you see after you've already committed to a state change.
Windows tends to keep their hover states strictly to tooltips, infotips or their equivalent. So, extra information. They believe it should "never require users to click an object to determine if it is clickable. Users must be able to determine clickability by visual inspection alone". Hover states help prevent unneccessary clicking, but they are still only discovered when a user already has the intention to click. This is why there's only a sparse amount of hover states used. A strong visual cue for interactive elements is preferred.
The lack of hover affordance is bolstered by the fact that Windows tends to be used in a lot of different environmental contexts, and a lot of those don't involve a mouse.
Not all Windows environments have a mouse. For example, kiosks rarely have a mouse and usually have a touchscreen instead. This means that users can perform simple interactions such as left-clicking and perhaps dragging-and-dropping. However, they can't hover, right-click, or double-click. This situation is easy to design for because these limitations are usually known in advance.