because screen resolution isn't solely dependent on screen size, in fact a 1080p screen, whether it makes 24in or 85in will always have the same number of pixel. Pixels gets bigger with a bigger screen if the screen is made to represent the same resolution, but as technology evolve it's possible to make smaller pixels and build cheaper displays with hose smaller pixels.
Meaning that 3ds being a newer generation gets a higher resolution screen, with smaller pixels instead of using a much bigger display.
FYI the measurement of pixels size compared to the display size is called the pixel density. (yes, the 3ds has a higher pixel density)
there's 2 ds display mode on the 3ds, unscaled and scaled.
Unscaled (the small one): gives a pixel to pixel display reproduction (1:1) but since the 3ds have 240 lines while the ds only have 192, it means that 48 lines will be unused
Scaled(fill the screen): the 192 are spread accross 240 lines (1:1,125),but the problem with this mode is that the pixels can't be subdivided meaning that you loose picture crispness and precision.
http://www.3dsbuzz.com/wp-content/uploads/2010/09/DS-on-3DS-Yoshis-Island-DS-comparison.png