I think it's legitimate to tweak an audio component to your liking. It's not always necessary to exactly know what physically causes the desired effect to make use of it, but it may be useful nonetheless to question it -- since the accumulation of false, impressive short-term effects can lead to a sonic result that will not convince in the long run.
I've tried removing the foam with my HD 580 and my HD 600 -- replacing it with nylon gauze --, and I have become an advocate of this tweak. But after a source change it (the HD 600) sounded better with the foam back in place. There are two factors in play: Sound passing a foam or fabric gets slightly changed and muffled by nature. This effect may be well known from speaker protections. On the other hand there's the beneficial effect from foam and other matters with slight sound-absorbing properties: They can help to reduce reflections on the speaker baffle -- and even from the moved air back to the driver membrane! --, thus make for better sonic contours and transient response.
In the case of headphones said beneficial effect is even more beneficial: The sound waves radiated by the membrane are reflected by the listener's outer ear back to the headphone driver and from there again back to the outer ear, etc. A thin piece of foam makes quite a difference in this scenario. And it's easily audible if you know what to listen for. The higher clarity and brilliance without the dampening foam comes at the price of a tendency to shrillness and softening of the first wavefront with transients, with the result of reduced accuracy and especially reduced depth of image -- everything sounds relatively close, the differentiation between instruments playing further back (thus with a relatively high content of reverberation) and the ones playing in the fore gets somewhat blurred.
That's not the only downside in the case of the HD 580/600/650. If you have a closer look to the innards, you'll notice that the baffle (the surface where the driver is mounted) only consists of a grid covered with fine mesh. It's actually sound permeable, so the design can be seen as totally open, like e.g. the Sony MDR-F1; there's virtually no isolation between front and rear of the driver. This causes the sound waves from both sides, with their opposite phase, to cancel each other -- the further down the frequency range, the more. Of course that's calculated in the over-all design, so don't think the Sennheiser developers don't know what they're doing!

But one thing has to be considered: The thin foam pad makes for a slight, but noticeable acoustic isolation between front and rear. So removing it has the consequence of not only increased brilliance, but also decreased bass. Head-fi member
j-curve has done some
measurements which prove this.
BTW, in my now system -- with HD 650 -- I tried the foam-pad mod several times, but found it to sound worse than the original configuration. I prefer the tightness and control the foam pads provide, as well as the better coherence and spatial reproduction. In the end it's a matter of taste -- and of the own system. Nothing wrong with trying and preferring it -- I'm guilty of this myself.