Ok, according to the manual, the engine will load the fxo file even if the accompanying fx is referenced in the script - in case the fxo timestamp is newer.

What will happen when both fx and fxo are in a wrs resource? I assume we won't have a timestamp there..?

Do I have to kick the fx files out of the wrs or will the engine take the fxo files autoamtically?

This does not completely answer your question but you can exclude file types for the *.wrs via the GStudioX->data->options.scr file (as you probably are well aware).

When both are in a wrs resource, I suppose the .fx file is used because it is not older than the .fxo file. For including in resources I would use the .fxo files only, and leave the .fx files out of the distribution.

If I try this, the script will complain that it cannot find the fx files (same goes for unresourced fxo). It only seems to work if I replace all .fx references in all scripts with .fxo ... which I want to avoid.