Hard to tell. The only traces should be the DS profile (the exploit data in the NVRAM) and to a way less evidential degree the play history in the activity log on sysnand (I ramped up 800+ hours in system settings now, I must really love it

). The NVRAM profile gets cleared when starting a DS cartridge (retail or flash cart), the activity log with a system format.
There might be other traces, and you wouldn't be able to remove anything if the 3DS bricks anyway. So in the end we'll have to wait if some reports come in akin to the "Softmoded Wii repair is 280$" fiasco.