It’s a huge problem. The most common approach to address it is called smearing; the duration of each second for a 24 hour period ahead of the “leap” is adjusted. For strict ordering systems this works as each device maintains time sync with the global clock, the duration of a clock cycle is just slightly different. I think this was in the original Spanner paper, actually.

Some rare systems use monotonic oscillator seconds and ignore the earth rotation second, but if you ever have to translate those to real time, you get an accumulating disaster over time and it’s generally regarded as not a good idea.

Leap seconds are not added on a regular schedule like leap days, they depend on physical measurements of Earth. So high reliability systems with comprehensive timekeeping would not be perturbed by these choices, I would think.