It's just my hunch, but I think if there's a real issue here it's more one of alignment than strictly the thickness of the cart. I've noticed that when inserting a retail cart, there's a very definite mid-insertion notch that makes sure the cartridge is properly aligned before it is fully inserted. With the Supercard, due to a combination of the cart's thickness plus the extra width at the top of the 3DS slot (to accommodate the tab on 3DS carts), the cartridge has a lot of side-to-side wiggle room, and the mid-insertion notch is less noticeable and holds the cart less securely. Because of these issues, it looks like its possible to jam the flash cart down into the bottom of the slot without being correctly aligned. The same potential for damaging the pins may exist while pulling the flash cart out as well. (?)
Until I have reason to believe otherwise, I think the SDS2 is safe so long as you're very careful to keep the cart going in the slot at exactly a perpindicular angle, and take care to feel for the mid-insertion point before gently clicking it down into the fully inserted position. And of course, exercise the same level of care when pulling it out.
(Note: this is just my opinion. I could be wrong. You could do your best to follow this advice and still screw up, and it won't be my fault.)