Windows won't show duplicate SSIDs for the reason you described. They are multiple APs broadcasting the same SSID to increase coverage area, and allow for roaming. Windows treats this as one network for a better user experience, based on the wifi chip and driver it will choose the most powerful signal with the same SSID. There is an option for this under your wifi chip advanced settings, usually called 'roaming aggressiveness', which defines how often Windows will prefer to switch to a better AP.

As for other networks not showing at all in Windows, I think you may be right. I've had weak networks not show up unless I disable wifi for a few seconds and enable it again.