Don't get me wrong, I'm not saying it's not a problem. It should be fixed.
But if you need a single system to stay up for 3 years straight that's probably not good. There's too much going on in a modern high tech server for that to be a good idea. Everything has a CPU in it (including disks, video cards, network cards, etc). And any of that could make your system unusable by hitting some rare condition.
> The problem is, if we can't expect software to run essentially forever, to update without 'restarts', and so forth, how are we ever going to achieve neural chip implants, artificial organs, synthetic agents mining ore in outer space, and so on?
I would hope such things to be purpose-made and to be made in a way that the user can survive a reboot/firmware update. Eg, your neural implant should be built in such a way that it's not going to be life threatening if the battery runs out. The system has to be designed with that accounted for.
Maybe there's a secondary, minimal implementation acting as a backup and keeping critical functions working while the fully featured one is being updated. Hopefully everything is implemented in a failsafe way so that if it completely stops working you're not in a worse state than before you got it.
Any plan where there's a crucial component that must not stop even for a second isn't a very good plan.