It not recommended to scan Domino data Directories with a standard OS level Anti-Virus program, this also applies to the Notes Traveler server. It is recommended to use a specialized scanner designed to scan mail and protect the Domino directories. Lotus Protector is one such product and there are many other third party mail security applications.
That said, unless the Notes Traveler also hosts mail files, no user data is ever stored on the Notes Traveler server, so it is not necessary to deploy a mail scanner on this system. All the emails sent from Lotus Notes Traveler mobile devices are delivered using the user's home Lotus Domino mail server. If that Lotus Domino mail server is unavailable, the Lotus Notes Traveler server will attempt to find an alternative if one is available as part of a Lotus Domino cluster. As such the anti-virus solution configured for Lotus Domino home mail server is used for scanning all the emails sent by Lotus Notes Traveler.
It is also advisable to have an anti-virus installed on the user mobile devices as an additional layer of protection to prevent any malware infecting the device itself.