Does merging reduce quality?
No. Merging copies page objects from one file into another: the same fonts, images and vectors, at the same resolution. A page that was 300 DPI before is 300 DPI after.
The file size is roughly the sum of the inputs, minus a little where fonts are shared. If the total is too big to email, compress the merged file afterwards rather than compressing each part first.
What happens to bookmarks, links and forms?
Bookmarks from the source files are kept and nested under an entry per file when you turn that option on. Internal links that point within a document keep working, because the destinations come across with the pages.
Form fields are copied, but two files with fields of the same name can collide in the merged document — the value typed in one appears in the other. Flatten the parts first if they are filled forms.
What if the pages come out in the wrong order?
Nothing is lost: open the merged file in Organize PDF Pages, drag the thumbnails into the right sequence and save. It is faster than merging again, and it is the same tool for deleting a duplicate cover page or rotating a stray landscape scan.
For a two-sided scan where one pass came out backwards — fronts in one file, backs in reverse — that is a different job, and there is a tool that interleaves them properly.