Thank you, dan long, this was a very nice answer to my question! *happy*
First, the literature that I read was Gaia's Garden, predominently. Certainly Toby Hemenway explained everything correctly so I guess I din't use the right words. I am still just at the beginning of my permaculture studies.
Second: The impression I(!) got in this book though was that the more fertile and richer your soil the better. Without any exception, pretty much like a principle (if not even a dogma). I understand the concept of mulching, composting, enriching soils when you start with a garden. Most likely you'll have to recover the land from former use. This is why you should enrich soil. And in a well established garden design you compost right in place and that's mostly it. But still, in this well established garden, with rich soil and everything, how would you grow beans? Wouldn't the conditions for my beans be unsuitable pretty much everywhere because of my mulching, my in-place-composting, creating compost tea when it rains and so on, my not-disturbing-the-soil-policy?
Also I want to say that the place where I grew my beans this year was in the corner of a raised bed, totally no competitor plants around. The raised bed was filled with 4 layers, on the bottom with branches, then a layer of lawn from the place where we build the raised bed, a layer of relatively fresh horse manure, then the top layer of good veggy garden bed soil I purchased from the store and finally I mulched with wood chips and shavings from the guinea pig cage (full with their manure, too). So I think I've got nitrogen rich soil underneath and predominently carbon (full with mycelia and fungy!) on top. Could it be that this is the reason the beans didn't really grow there and were full with black aphid? Had I created an excess of nitrogen in the soil? Is it then that it's never a good idea to grow beans in a newly build raised bed? Well, this particular one was already 2 years old by the way but still I guess there was a lot of nitrogen left...
And about my initial question "Over-fertilizing":
Does this term only apply to plants growing in the wrong spot? Like when there is too much of nitrogen? That's what I understand from this anyway. I am still left with this question: As plants are most likely not forced by anyone to "eat" all the nutrients available what is the concept of "over-fertilizing" a plant?