Couldn’t resist 
After reading the linked infos I added
extern volatile unsigned long timer0_overflow_count;
to my sketch and after the deep sleep I inserted
timer0_overflow_count += 3E6;
Thats it! timer0_overflow_count comes from wiring.c in the arduino core and is used for micros().
Adding at least 3E6 microseconds did the job. Could be adjusted depending on the real sleep time.
Sounds so easy - did I miss something? Maybe there will be some trouble when micros rollover.
With this modification my node now needs less than three seconds for wake up, doing some measuring, sending data and going to deep sleep again.