PC suite mode is just a bunch of serial to USB devices.
In Ubuntu you need to change the udev rules in order for a normal (non-root) user to access these devices.
That is the reason that by default only the DUN over USB connection can be used in ubuntu through the network manager (that service has the proper permissions).

By default the N900 runs an OBEX file server and client through USB and Bluetooth. So you can use that to send files though OBEX. (don't know how to do that using C++, but you can also use linux command line tools or python libraries).

The N900 also runs an SyncML server and client through USB and bluetooth, but that is only intended to sync Contact, calender events, tasks and calender notes.

If you enable USB networking mode on the N900 then communications becomes easier, because you can just interface to any running networking service through this network. (But most aren't installed by dedault, but SSH, NFS, SMB and SyncML over IP client and servers are available in the repository).