Of course if waking from deep sleep is always done from the reset feedback then the wrap-around can't occur but if it is done via an external trigger (e.g. from a sensor) then the period can be very long.
I think the counter is actually a 31 or 32 bit counter (not 64) but it is running from the slower "RTC" clock so the wrap around is around 3.5 hours. The software translates the counter into microsecond units with a 64 bit value.
One can always think of ways a design could be "improved" but one also has to be very careful that any changes that are made don't break any software out there that relied on the previous behaviour.