Well, we just log the info, average user may not even see it, but i think it is useful to have something written because we modfiy configuration file format.
Also it documents what is the upgrade hook for for developpers.
We could use a single comment (for devs) but since we have to write it (and if we don't mark it for translation), why not output it ?
It may help if bugs arise and for users doing weird things with their Picard configuration file.
Regarding the `log.info()` vs `log.debug()`, i would say to keep `log.info()` as this code is normally executed once only, and debug isn't enabled by default (if this code was run each time  Picard starts, i would use `log.debug()` for sure). As such, and as i think keeping the user informed of what happens behind the scenes (as it may have an impact on, ie., an external script) is needed here, `log.info()` seems better here. Moving this info to `log.debug()` means essentially hiding it, so better to move it to a comment in this case and don't bother with `log`.
I followed what was made before (ie. first upgrade hooks is interactive with dialogs and questions to user .... nothing "internal implementation").
Overall i don't think a single line of log is an issue for anyone.