Batch conversion of Waters mass spectrometry file formats
Waters Databridge actually allows the conversion of multiple files at the same time, but somehow it is not very intuitive to use (not a native UI) and also does not really work in batch mode. Still, it is somewhat possible to quickly export Waters .raw files using Databridge, and it is the best solution I found so far. From there, a simple python script allows me to average the mass spectra (that are still chromatograms), so that it at least doesn't take hours to export every single mass spectrum by hand.

For other people in my position, having to convert hundreds of Waters .raw files, I hope that helps at least somewhat.