In the YouTube help section "How to optimize video uploads" it states:
"If letterboxing is added to a video before it is uploaded (to create a 4:3 video from a 16:9 master for example), the widescreen player will add pillarbox bars too, resulting in black bars all around the video (windowboxing) and a bad viewing experience (see the diagram below)."
I didn't know what "windowboxing" was until I inadvertently caused it myself on some of my own video uploads. I've since figured out how to avoid windowboxing by rendering my videos at their original source aspect ratios before uploading.
If however, the original aspect ratio fed into your rendering software comes from a video source and capture device that already includes pillarbox and/or letterbox bars, then you'd have to edit these out with the cropping feature of the software and render to the cropped aspect ratio. I use Sony Vegas for this, but I think there is free software that will do the same.