Bits of pieces of the operating systems might handle leap seconds properly, but it's doubtful that every single component that uses time does the right thing. The last two leap seconds have revealed bugs in the kernel: https://lwn.net/Articles/504744/ for the one in 2015 and https://lwn.net/Articles/648313/ for the one in 2016, and I don't think it's unlikely that the one scheduled for December will reveal another.
Some things did go wrong on a few of the previous leap-second injections, and the Linux timekeeping maintainer had talked about changing the approach to handling them (which has already changed at least once in the past).
I don't, however, think it makes sense to unilaterally change this, without (any obvious signs of) coordination with the timekeeping maintainers and the maintainers of major NTP servers.
Things go wrong on every leap second, sometimes catastrophically. They go wrong on non-leap-seconds because of falsely advertised leap seconds. They go wrong 4 months before a leap second because a leap indicator got set and some software had an incorrect idea of when it was due.
Never mind the theory, the practice is a clusterfuck.
I am sure tons of applications that use gettimeofday() to keep track of time can break in subtle ways when seeing 59 twice. Of course, they're broken considering that there is clock_gettime(), however this is a POSIX interface that is not really monotonic too by default, and the monotonic versions of it are Linux-only implementations.
> I am sure tons of applications that use gettimeofday() to keep track of time can break in subtle ways when seeing 59 twice.
gettimeofday doesn't return hour/minute/second divisions; it just returns seconds/microseconds since the epoch. Functions like strftime and gmtime handle the components of time. And leap seconds don't make applications see 59 twice; they make them see 60 once (58, 59, 60, 0, 1, ...).
Quoting the manpages for gmtime and strftime:
> tm_sec The number of seconds after the minute, normally in the range 0 to 59, but can be up to 60 to allow for leap seconds.
> %S The second as a decimal number (range 00 to 60). (The range is up to 60 to allow for occasional leap seconds.) (Calculated from tm_sec.)