The original colors were just Nintendo being amusing - the NPDP-reader was intended for development and was red (for Mario) and the NR-reader was for testing and was green (for Luigi). Developers quickly noticed that the distinctive color of the NR-Reader sometimes resulted in them being stolen at shows (the same thing happened with the debug PlayStations) - so it became common for people to swap the NR-reader drive into a retail cube for camouflage purposes when they were doing public demos.
Later on, Nintendo would start supplying retail looking NR-Readers on special request, but most of them were just converted by the developers.
The same approach carried on with the Wii - except in that case the white version of the RVT-R (wireless) that could pass for a retail was available pretty much from day 1.