I talked to a ME (mechanical engineer) friend of mine who specializes in carbon fiber about this - he said if there was a bidirectional weave, he'd have no issues at all drilling, it shouldn't matter. However, after looking at some articles about the manufacturing process for the i3, he said it sounds like the weave they use for the roof is unidirectional, and thus not a good idea to drill into.
FWIW - he suggested stripping paint away on the surface and using Hysol epoxy with as close to flush-mount/rail mounts as available, then repaint around (and use removable feet so racks can be removed). Apparently the peel strength # for hysol is higher than the base laminate of the CF itself... I haven't tried it yet, but it's an idea!
The SeaSuckers seem like a great solution if you only occasionally need racks. For me, I drive into the mountains almost every day with skis in the winter, and my car spends much of its winter covered in all sorts of road salt, so I'm not sure it'd work very well, and I need a daily solution, not an occasional thing.