There was a program recently on Star Trek(*) technology and its influence on real inventions, I believe on the Discovery channel. The section on the transporter and my experience in high security environments (the Pentagon, pharma research labs, etc.) got me thinking on the staggering implications such a device would have on physical security of sensitive facilities.
Unlike many current explorations of potential teleportation which focus on end-point to end-point transfers (between a sender device and a receiver device), the Star Trek "transporter" is end-point to anywhere and anywhere to end-point; you can step on a transporter pad and beam down to a planet surface without having to be reassembled by another transporter device. Similarly, you can "beam-up" from any point, regardless of whether a transporter device is present, to a transporter pad at the receiving end. In the later series, the transporter device becomes a mere facilitator in point-to-point transfers where there is no transporter pad at either the source or the destination ("two to beam directly to sickbay"). It is interesting to note that the recent tv special claimed that the transporter technology was introduced into Star Trek in order to reduce the special effects budget by eliminating shuttle landings from each episode.
In any case, the best data security is often maintained by restricting physical access to the network, terminals, work area, and data storage. This is, of course, dramatically altered when an attacker can materialize at any point inside your facility. Star Trek level sensors could probably do a decent job of tracking individuals inside the facility and recognizing when an unexpected one shows up (in many episodes, the sensors can recognize "biosigns" and even pick out distinct individuals). This would not do much good, however, if an object, such as an armed H-bomb were beamed in instead, or something more subtle such as a chemical or biological agent which might not be immediately detectable.
A sophisticated attacker might merely beam in a monitoring device, small and with low power requirements and thus hard to find. A confederate could even precisely place such a device without the risk of being caught at a security check point with unauthorized equipment. Instead of transmitting gathered data and risking detection, the device could be beamed back out later, or if this were difficult (perhaps pinpointing the device from a distance was not easy), the data could be encoded in some way, perhaps on bacteria that the insider could remove without detection.
[Of course the attacker would not need to go to any of these lengths if network security worked like it does in BattleStar Gallactica, where merely running a cable between two computers enables remote exploit.]
New methods would need to be invented to counter these threats. Perhaps the use of transporter technology could be strictly limited, but prohibition rarely succeeds for long. Deflector shields apparently stop transporter function, so critical facilities could be shielded, not to protect from bombardment, but infiltration. Some sort of "transporter-lock", a method of raising and lowering shields in sequence to allow personnel egress and entry would need to be devised to prevent exposure. This would likely be hideously expensive due to energy constraints. Perhaps certain materials could be devised to block transporter beams, although in the series, transporters are used in a variety of circumstances, including beaming into deep underground caverns. Maybe the old standby, a Faraday Cage, would be sufficient to make transporting difficult or impossible.
In any case, I doubt this will be a worry in data centers any time soon. My imagination will almost stretch to accept that end-point to end-point teleportation may happen in the next few centuries. End-point to anywhere teleportation seems a problem of an entirely different magnitude.
(*) Star Trek is a registered trade mark of Paramount, yada yada yada.