You can try np2kai (an emulator for Japanese PC-98) on 3DS to play many of the same games and you will see what a problem the resolution is. Bilinear filter helps a bit, but it still doesn't look great downscaled onto 3DS.
Most X68k games use 256x240 resolution.
Where did you read that?
from Wikipedia Sharp X68000 specs
Screen resolutions (all out of 65,536 color palette)
256×240 pixels @ 16 to 65,536 colors
256×256 pixels @ 16 to 65,536 colors
512×240 pixels @ 16 to 65,536 colors
512×256 pixels @ 16 to 65,536 colors
512×512 pixels @ 16 to 65,536 colors
640×480 pixels @ 16 to 64 colors
768×512 pixels @ 16 to 64 colors
1024×1024 pixels @ 16 to 64 colors
Most games I have tried on PX68K (eg the below golf game) run at a resolution of 512x512 (for maximum colours) and this resulted in very ugly downscaling on some platforms that rendered the image unreadable. Using correct aspect ratio stretches image horizontally by a factor of 1.375 to become 704x512.
As a reminder 3DS has resolutions of: 400×240 (top) and 320×240 (bottom)
https://refuge.tokyo/x68k/x68000/00380.html
full list of games with screenshots:
https://refuge.tokyo/x68k/x68000.html click the "English" flag