thank you for your reply. Initially we tried to run mongo repair with root, that changed the permission of the folder (wrong choice).
At the end, after a permissions revert, we were able to restore the db with this command:
sudo -u mongodb mongod --repair --dbpath ./data/db/ --storageEngine wiredTiger
But first we had to set this rules in /etc/security/limits.conf:
* soft nofile 512000
* hard nofile 512000
* soft nproc 256000
* hard nproc 256000
I don't know if the reason is that we had 140k collections, but before to set the new limit we got the "too many open files" error also in the repair procedure as well.
Last details: when the db got repaired, on the server reboot we had to wait more than 10 minutes to have mongo finally up, but luckly it worked