I know it by seeing it. when it uses the exact amount of pixels as it was designed for. you easily see that if the picture is washed out/blured/interlaced etc. -> not native. or if each pixel is crisp and clear perfectly displayed as it should be.
the 3DS has a 400x240 WQVGA x2 screen. so it displays any 320x240 or 320x224 designed games (which most of the sega 80s games were) pixel perfect either in full height or with a bit of a filler on top and bottom and cut of 40 pix on each side.
All three so far released super scaler using 320x224 native resolution. I think, but i have to check this again, they have even expanded the horizontal resolution to meet the max vertical resolution of 240 by adding more of the graphics oin each side. in this case this would be something like 342x240 uneven.