ext4 moved some time ago to 30 bits of fractional resolution (on the order of nanoseconds) and 34 bits of seconds resolution. It punts the problem 400 years or so into the future. I'm sure we will eventually settle on 128-bit timestamps with 64 bits of seconds and 64 bits of fractional resolution, and that should sort things for forseeable human history.
That is roughly 585 billion years[1].
[1]: https://www.wolframalpha.com/input?i=how+many+years+is+2%5E6...
I wonder what the zfs/btrfs type file systems do. I am a bit lazy to check but I expect btrfs is using 64 bit. zfs, I would not be surprised if it matches zfs (edit meant ext4 here).
So 580 years or so till problems (but probably patchable ones? I believe the on disk format is already 2x uint64s, this is just the gethrtime() function I saw).
https://man7.org/linux/man-pages/man3/timespec.3type.html
it is convenient unit because 10^9 fits neatly into 32 bit integer, and it is unlikely that anyone would need more precision than that for any general purpose use.