[I'd be careful with that document, by the way. I can't find a definition of "update"(Jan 2012) vs. "revision"(Aug 2002), but either way, there's plenty of information on-line that's known to be up to date versus trying to figure out what's going on there.]
For example, if there is a graph showing some data which is detailed on the the page contents, any alt value other than the empty string would be redundant.
This is not true. Alt text is intended as a replacement for the image it's applied to.
If the image is primarily decorative(a slightly better term), then yes leave the alt blank because it doesn't really convey much "information" to, for example, blind users.
Your example situation is much more case-by-case, but if your text says something like "survey data show an increase over time as in fig. 1" the alt text should be able to replace the image altogether. It should read something like "graph showing increase of [data] from [x value] to [y value] over [timeframe]." so that, for example, a blind reader actually gets value from it. If your text goes over the graph contents in great detail, then maybe you could get away with not doing that. But realistically, screen reader users deal with this all the time, can recognize the duplication, and have tools to skip and so on.
Sometimes, the alt just repeats content alredy covered in the page contents
You're interpreting the situation incorrectly.
Yes, as you describe this, it would probably be better to leave that alt text out. But because that alt text sucks, not because it shouldn't be there at all.
Ideally, what you should do in response to this situation is provide better alt text.
In those cases, alt="" would prevent anything from being rendered, and the page would actually look better on Lynx.
"Looking better" as any sort of consideration for alt text is a sign of missing the point.
[would] a website suffer any penalty in terms os SEO if alt="" is used on some of it's images
Penalty? No. The only possible assumption for empty alt text is that it was left out because unnecessary. It's a neutral situation.
Or it would be better for ranking to keep every alt, even if redundant?
Don't make your alt text redundant, anymore than you would repeat a paragraph of body copy.
Alt text is content even though you usually don't see it.
On the other hand, if you can't commit to creating decent alt text, then sure it would probably be better to just leave it out, rather than, for example automatically sticking the image filename in there, as some applications do.