There several free image editors out there, such as Gimp, Krita and MyPaint. They are all capable of putting together two images side by side, but the actual actions will all be slightly different. Usually, the metadata of the base image (the one you load first) is kept.
If your images are scans, there is not much metadata. You have the resolution (but this is useful only if you want to print the picture at the very same size), possibly some Exifs (Digitized Date), but way less that with a camera. Otherwise I assume that you have added descriptions or other tags manually? In any case EXIF/XMP/IPTC do not define how to store metadata for several pictures, so you will have to chose. The metadata of the back scan is possibly a bit less important. If this is critical, there are ways to merge the metadata of one picture into the metadata of another (I don't know is the software already exists, but this can be written as a script based on utilities such as ExifTool). A variant of this is to copy the metadata from one of the source images to the composite image (utilities such as ExifTool can do this), so you don't have to worry about metadata support by the image editor.
Decent image editing software lets you set the JPEG encoding parameters. There are two distinct parameters:
- Chroma sub-sampling: JPEG considers that our eyes are much more sensitive to luminosity than to color, so your RGB image is decomposed into 3 images: a Luminosity one and two "chroma" ones. The chroma images can have their size reduced (halved or quartered) and this alone can drastically reduce the size of the file (and has minimal visual impact).
- Quality: the one everyone knows. Quality in the 90-95 range is usually enough. The real question is the actual quality used by the scanner software if it produces JPEGs.
The small size of your output files is probably more the result of a reduced chroma than of reduced quality, but this is just a guess. The best way to tell what happens to you files is utilities such as ImageMagick's