More likely is that the repairs crew don't care about the warranty. The office people do the warranty worrying, the repair crew will simply reflash your DS right off the bat with the latest copy of the official NDS BIOS and THEN begin testing on the unit. They do this because A) it eliminates any problems that may only be due to defective BIOS software (whether by corruption/"illegal" flashing or design fault) and it is also;
It is quite likely that they temporarily install a debugging BIOS onto the unit as well to determine if there are any hardware defects before even opening the unit. The reason I know this is because they use the same repair techniques that phone repairs people do. This is why most of the time when you receive your phone back from being repaired all the settings and data seem to be erased.
The only time this will really matter is if one of the repairman has had a particularly nasty day and feels grumpy and sends your unit back saying it is in breach of warranty. Very rare but worst case scenario is that you tell them to hold onto it and that you'll agree to pay for the repairs. That'd have to be one hell of a bad day though. =P
Have a nice day.