Physical contact is one thing and I could go on for hours about it; suffice to say I presume in most cases it would take a significant amount of cutting and ripping away support equipment to actually reach the capsule. That's my thought, though.
Regarding data: I'm not doubting there are data links from the ship running in and out of the capsule; there absolutely have to be for the data flow. My questioning was more 'why wouldn't there be several layers of significant protection between the brain burner/termination and anything receiving information from the outside'?
For instance:
- Would externally connected subsystems even share control equipment with the burner/termination pack? Given the value of getting a capsuleer home alive, I'd be very surprised if there weren't independent backups for those systems.
- Would externally connected subsystems be programmed to allow commands to be received from an external port? Not being a software science person, I would feel that this be the flimsiest wall of electronic defense - but I'd be shocked if this kind of thing didn't exist in some fashion.
- Is the external connection equipment even configured to allow commands to be transmitted in? Remember, the only people with a vested interest in maintaining an override - CONCORD - can do so from within the pod.
Well, I think there would be some significant protection for the data lines, certainly. But if you're boarding a ship, you're not probably using the front door, so we're probably assuming you've already cut your way in. It can't be impossible to get at the data lines, since I'd assume just from experience that you'd need to be able to get into them for maintenance. If you're on a spaceship that contains people, detritus is going to eventually get into places you don't want it to be, if nothing else. It'd probably be difficult, but I can't imagine the lines are that deeply buried that you couldn't get to them at all.
Protecting the capsuleer with some kind of insulating software might also be an issue, but not necessarily a big one. Suffice it to say that a signal would have to go to a camera, for instance, take the image the camera is showing, and then send it back. Like an online download, there's no way of knowing that all the data coming from the camera is coming from the camera if something gets in the way. It's just a signal that probably gets translated into data the brain can understand. There's no reason why that same data couldn't register a noise so loud in the brain that you can't think anymore or throw the brain into a seizure.
There's always the possibility that the capsule will always prevent that sort of thing if it comes down the line (like a flare compensator in a camera, for instance), but in that case I'd say electronic warfare is even MORE of a possibility. After all, that means there's something between the capsuleer and whatever is receiving signals that's making decisions and has to be fairly universal between all existing ships. In that case, it would be theoretically possible, if you can get into the data, to simply flood the computer with gibberish and crash it. I guess the BSOD is something else that probably happens semi-routinely in the EVE world that they don't make us deal with for game reasons.
So on those three points:
1. I think the brain burner is probably not only something that would be most heavily protected, but the hardest to hack since it's tied to something that can be monitored directly from the capsuleer himself (vital signs) or the capsule alone (the state of the capsule). Ejecting the pod probably isn't as difficult, because that requires input from the ship, some parts of which are very far away, and requires activating ship equipment to eject the pod. That's why I'm saying it would probably be more likely to eject the pod (or to keep it from ejecting if you had the time or programming to do that, since that's a good way to make sure you've got time to work on the pod if you know your capsuleer isn't going to deep fry his brain to escape somehow). But yes, making the scanner fire to fry the capsuleer in the pod is probably not something you can do very easily from a remote part of the ship. It's an autonomous part of the capsule.
2. This is one of those things where you'd have to take a wild stab at how computers work in EVE. There is probably some manner of encoding that would make it more difficult to interfere with the signal, but that's counterbalanced by EVE's need to have a capsuleer be able to use any ship they have learned to fly themselves. Therefore, you can figure that any specific make and model of ship would interact with a capsule in a logical and predictable way. It's one of those things that could go both ways, though. Maybe encoding is so complicated that there's no way to decrypt the signal in time, or maybe it's as easy as hooking a portable AI in and giving it a few seconds to work out which combinations are sending what signals it knows must be heading to the capsule. I'd imagine it's somewhere in between, that if you got into a ship and spliced in, it's probably going to take a minute or so, but it wouldn't be entirely alien. That may also depend on if the capsuleer decides to dick with his own computers and writes his own encryption. That might make it harder or less stable to interface with depending on the computer skill of the capsuleer, but would probably make it a lot more difficult to break in. It's harder to break into a custom Linux system than a Windows computer, after all, just because compatibility issues means you'll know what you're getting into on a PC.
3. I think this is almost a guaranteed yes. Just taking the aforementioned idea of a camera into play, you're talking about pouring data into the visual center of the brain, telling it what it is "seeing". Anything going into the capsule is transmitting some kind of command to do something, and that's not even going into what it can do from outside the pod. Certainly, commands run all over the ship to make sure the capsuleer can fly in place of a few hundred crew members, so anything automatic that takes a cue from elsewhere is fair game. To that effect, though, not all commands and lines are created equal. I'll assume that it's not every power cable that you can tell to fake a destruction signal to the pod to command it to eject. I would assume that the line for that isn't hard to find, though. Knowing everything that might happen to your ship means having lots of little sensors everywhere to say when a catastrophic hull breach is about to turn your ship inside out.
All of this is assuming that the capsuleer has a lot of external and internal control over the ship. If a lot of it is handled by shipboard crew and most of what the capsuleer has to handle is outside the ship, I'd imagine the capsuleer would be more insulated from that kind of thing. They'd also have a lot less control over what was happening inside the ship. Since you can't board in-game, it's hard to say either way. This is all speculation, of course.