All you need is a toolbox and some spare time, even if the device was bricked.
On the core rulebook, page 228:
Repairing Matrix Damage
If you have a device with Matrix damage, you can repair
it with a toolkit, an hour of work, and a Hardware
+ Logic [Mental] test. Every hit you get can be used
to either remove one box of Matrix damage or cut the
time required in half; the first die spent toward time reduces
the time to half an hour, the second to 15 minutes,
and so on, to a minimum of one Combat Turn (3
Bricked or not, the device is off-line and unusable
during the repair process.
If you critically glitch on the roll to repair your device,
that’s it. The device is permanently bricked. You can use
it as a paperweight, an object lesson, or (if you need
one) a brick. If you glitch, the device can be restored to
functionality, but it becomes a bit glitchy (the gamemaster
will tell you how at an appropriate moment).
Implanted cyberdecks should be easily accessible, otherwise there is no point in implanting them, you will just have to spend thousands of nuyen on shadow clinics every time out get out of a cyber combat.
This issue is further discussed on reddit, on shadowrun's forums, and on dumpshock's forums.
Aaron gave us this answer on dumbshock forums:
I think it will eventually be made clear that cyberware has one or more external ports for maintenance.
But basically, you will need either a datajack to access your cyberdeck, otherwise you cannot even manually reboot it as you would need to split your body open to reach his on/off button. Or follow the description given by Drake Noble on SR's forum:
As for repairing matrix damage - implanted devices that need repairs (or upgrades) like a commlink or a cyberdeck are actually (according to Shadowrun back when they actually told or showed you this stuff clearly enough - so SR1 & 2) installed on a "plate" attached to the outside of, or replacing a section of, the skull... which means the parts that need repairs to clear up matrix damage are actually close to the skin.