Here are some answers:
/dev/serial/by-id:
total 0
lrwxrwxrwx 1 root root 13 Mar 30 21:47 usb-Arduino_LLC_Arduino_Leonardo-if00 -> ../../ttyACM0
/dev/serial/by-path:
total 0
lrwxrwxrwx 1 root root 13 Mar 30 21:47 pci-0000:00:1d.0-usb-0:2:1.0 -> ../../ttyACM0
crw-rw---- 1 root dialout 166, 0 Mar 30 21:47 /dev/ttyACM0
I have no usb-related stuff in /etc/udev/rules.d/, just the default 70-persistent-cd and 70-persistent-net, and none of them contain 2341. I also noticed that in /lib/udev/rules.d/77-mm-usb-device-blacklist.rules the Arduino devices are mentioned at the bottom of the file (this should prevent them to be taken by modem-manager).
# Arduino devices, FT-232-based series and Atmega8U2 (Uno)
ATTRS{idVendor}=="0403", ATTRS{idProduct}=="6001", ENV{ID_MM_DEVICE_IGNORE}="1"
ATTRS{idVendor}=="03eb", ATTRS{idProduct}=="204b", ENV{ID_MM_DEVICE_IGNORE}="1"
ATTRS{idVendor}=="2341", ENV{ID_MM_DEVICE_IGNORE}="1"
I forgot to mention (just for completeness, it doesn't seem to make much difference) that the dmesg of my previous post comes from a PC with native Lubuntu 12.10, while the same on the Lubuntu VM only shows the second connection (the first connection is managed by the host OS). All the rest (devices, rules, lsusb output) are the same.