Kah! Your answer led me to 2 problems:
first is the main one, comparing to docs, I saw no problem with my crontab command so I launched it without the logging part (so it output directly in terminal)
answer is: Piwik Console is known to be not compatible with PHP-CGI (you are using cgi-fcgi). Please execute console using PHP-CLI. For instance "/usr/bin/php-cli console …"
witch lead to the second problem: documentation is out of date (^_^; )
1st problem resolved by replacing php5.5 in command line with php5.5-cli
/usr/bin/php5.5-cli -d memory_limit=512M /path/to/stats/console core:archive --url=http://piwik.domain.tld/ > /path/to/stats/piwik-archive.log 2> /path/to/stats/piwik-archive-errors.log
witch repopulated stats.
2nd is up to piwik team =]
Thanks for the help
edit: now this is weird: only graphs have been populated:
[attachment 1920 piwik2.png]