It doesn't really matter if the last three digits are just noise for the time being. It's just as practical, from the programmer's standpoint. 64 bits worth of nanoseconds gives abundant range (±292 years from the origin) and microsecond times already necessitate a 64-bit representation (2^31 microseconds only gets you half an hour). So you can build all your protocols around signed 64-bit nanos from a defined origin and never need to change it again.
This has already happens. OUCH and other binary protocols have carried nanoseconds for years. FIX now specifies microseconds be supported in all time stamps but also lets you use nanos or even picos if you and your counterparty really want to.
The protocols might had ns resolution, but that doesn't say anything about the accuracy of the time information in there. The PPS output of GPS receivers typically has a jitter of a few ns. And how well is the position of the antenna known?
