Here’s some additional options that you can pass when using pdfwrite as your device. According to that page if you don’t pass anything then -dPDFSETTINGS it gets set to something close to /screen, although it doesn’t get more specific. You could try setting it to -dPDFSETTINGS=/prepress which should only compress things above 300 dpi.
gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile=out.pdf in1.pdf in2.pdf
Another alternative is pdftk:
pdftk in1.pdf in2.pdf cat output out.pdf