I love how the "y cant i make the screen fit?" question is asked in nearly every jEnesisDS thread I see. Pretty sure it's in the ReadMe file somewhere.
The software-based renderer version that Vague Rant was talking about is v0.4a I believe. Go download that and give it a shot to get an idea of what must be sacrificed in order to get horizontal scaling in the emulator, namely sound and speed. It does however have two different blending modes that make the scaled graphics look better for various games.
The reason for the difference is simple (well, sorta). Almost all versions of jEnesisDS use hardware rendering, that is, they basically translate between the dedicated 2D hardware systems of the Genesis and the DS. This means that the DS spends very very little CPU time actually drawing to the screen, because the DS has already taken care of handling the sprites and background layers and transparencies and priorities using its own 2D hardware. The DS doesn't really know what the screen looks like at any given time, since it's almost blindly executed the draw commands it's been given. Now the DS's 2D hardware draws to the screen line-by-line, so you can scale vertically simply by skipping a line here and there. Doing the same horizontally is not possible.
The DS also contains a single "framebuffer" mode in which the screen is mapped to a chunk of memory, and writing to that memory will change the colors of the various pixels on the screen. By using this, you can calculate in memory what the image is supposed to look like, then paint it to the screen pixel-by-pixel by manually modifying every byte in that chunk of memory. Since you know what the screen is supposed to look like before you draw it to the screen, you can modify it with things like scaling and filters and effects before drawing. But the process of updating the screen this way is very CPU intensive, affecting the overall emulation speed. Frameskip helps here because it lets the DS spend more time working on game logic and less time displaying the results to the screen.
Other comparisons: NES DS uses hardware rendering, NesterDS+ is more accurate graphically but runs much slower. Goomba Color for the GBA uses hardware rendering and thus can run at full speed on the GBA's 16 MHz processor, while it took several versions for Lameboy's software-based renderer to run the games at fullspeed on the DS's 66 MHz processor (also try the Goomba Color DS test build - if you turn off the frame limiter you get INSANE speeds). All SNES emulators for the GBA and DS use hardware rendering, which is why you can get full speed but also have such severe graphical glitches.
In short, hardware emulation gives you speed, software emulation gives you accuracy. With jEnesisDS, Lordus chose to focus on the former.