OK, so the answers are :

- time-based folder name : no, but shell can provide it (eg : `date +%Y-%m`),
- navigation index : no, but an php page could be use to list the sub-folders
and extract the date from their names,
- Symbolic links to save disk space : no, except with a zfs file system (see
post <http://forum.httrack.com/readmsg/22206/22205/>).

By the way this last post doesn't show up with a research on "archive", maybe
this response should be added to the FAQ ?
In case it could help someone, here's my cron script 

/usr/bin/httrack <http://www.mywebsite.net/> -O /var/www/mywebsiteArchives/`date
+%Y-%m`/ -%l "fr, en, *" -%U apacheUser -C0 -I0 -f2 -N "%p/%n.%t" -q