It is not that DOSBox purposely uses square pixels. With render set to 2x or 3x it is only doubling or tripling the exact same number of X and Y pixels of the original display. This gives it its unnaturally swished aspect over what it was intended to have. It is the sole reason that both DOSBox and ScummVM have the aspect correction option, to give it the same aspect for which the original artists created their graphics.
As noted, it may not make that much difference for new game development, but it is a real obstacle when working with original resources. Just for display having DOSBox set to use aspect correction is enough, but it would be great if the drawing canvases and any polygon tools had a switchable view. I don't know how difficult this would be to implement.
I agree it would be nice. I know DOSBox/Scumm isn't "purposely" using a 1x1 aspect ratio. If you correct for aspect ratio, things look blurry (in Scumm, at least - which is expected when you're scaling hard-edged "pixel perfect" graphics by fractional amounts. Presumably that's why it's not the default setting?). I can look into it for SCI Companion, but I don't think it would be a trivial change. The code is currently setup for integer zoom levels, changing it to floating point might be a bit destabilizing (i.e. a lot of bugs could come out of it).
[edit:] Ok, I looked into it. No promises, but it looked easier than I had anticipated. In the pic editor, at least, it was pretty trivial to implement.