Well hi first, been readinf for a while, but this is my first post. yay.

We've been playing with implanted foci since 2nd edition. Of course, back then implanting a focus was quite a bit more of a risk because of the grounding rules, but some of us, including me, were willing to take that risk because of the simply huge cost of foci. Loosing your powerfokus really kicked you back.
Not to mention the fact that a focus worked just as nice as blood when it came to ritual magic.
As for traveling via plane, beside the fact that most runners are unlikely to use these methods of transportation (kind of a sin problem... ), even if they did an implanted focus wouldnt be much of a problem. Just travel sub orbital and the company wont worry about mages that much. No astral space up there, so no spells.
As it was said before, there arent that much options to prevent a mage from causing havoc in a plane when he wants to. Airlines rely mostly on the idea that most dangerous mages want to get away with what they did, which is kinda hard on a plane barring parachutes.
For rules, we basically considered implanted foci to be a different type of fingertip compartment, which is 0.1 essence. This coupled with the fact that your going to loose magic along with it balanced things out in our opinion. And as mentioned above, there was the risk of having a useless piece of whatever implanted when the focus was destroyed. You did have to buy a focus specifically designed for that though. This also provided the GM with a simple option to beef up enemy mages without handing us a couple of hundred thousand whenever we killed one.
Weapon focus spurs, razors and similar things were also pretty common for us, though, in these cases we figured it's just the blade that's enchanted, not the actual cyberware that is connected to your nerves. Kinda like a switchblade. Again, the loss of magic balanced things out.
As for decompression, even today there are bullets specifically designed to enter but not leave the target. Basically the bullet enters and splinters inside the target, so airline security can take down threats without having to worry about blasting the walls (As long as they hit that is). Im pretty sure that 50+ years later these bullets would be refined and perfected. And besides, where does it say that security actually has to use bullets? If I had to design airline security, I'd equip everyone on a plane with a Superquirt instead of a real gun. That way you wont even have to worry about hitting innocent bystanders. A few hours of sleep never hurt nobody.