A lot of the software available for purchase through Apple’s App Store is also available for purchase direct from the developer’s website. Typically in these cases, you can also download updates directly from the developer’s website.
If you purchase software through the App Store, then later download and apply an update directly from the vendor’s website, it will likely confuse the App Store into thinking you’ve never purchased the software. This means it won’t show as purchased in the App Store, and will require re-purchasing it for future updates through the App Store.
So bottom line, if you purchase software through the App Store, keep those software purchases updated using the App Store.