Good Question ---
If your image editing software allows you to aquire the image from the scanner it will be a better image. In the case of Photoshop or Photoshop Elements you can import from the scanner and it will bring up the Epson Driver software pack, let you scan the image like normal and bring it back to Photoshop for final touches (cropping, rotating, resizing). By doing this you are taking some of the compression off the table.

If you scan to a JPG file, then bring into a photo editor (Photoshop Elements or Photoscape) you will have already compressed the image somewhat, then when you save again you compress further. Now a large image has some room for compression but still raw is better.