I agree. Adding spaces for span elements will change the semantics and likely affect other rendering in a negative way. For example, sometimes you may use span to style just part of some text or it could affect layout of things like icons etc. I note that neither chrome or firefox add spaces and will just run the text into the previous/next word if there is no space around the tag.
Having said that, I notice when looking at the example page you posted, there is no text running into previous/next text around span tags. This makes me think that the page is using a CSS style to style the element which is not honoured by eww/shr? I had a quick look, but it really is a very ugly piece of HTML. At any rate, perhaps the issue is not that span elements should have spaces added, but that eww/shr is not able to add the CSS style which adds the spacing to the span content?