I had Naza v2. and flight time was about 17-18min, recently decided
to try APM 2.8 3.3.3v for quadrocopter. After couple test i see that
flight time now is about 9-10 min, and extra weight only +50gr.
In my FPV screen when battery 50-55% I loose max throttle. Its
like not enough power to the engines and cannot take off again. Maybe i miss
something in configuration ?
It sounds like you have your battery failsafe set too high.
When the OSD indicates 50%-55% how much do you actually have to put back into the batteries when charging?
Is it 50% to 55%?
If this is the case then the numbers add up that you will get the right flight time, it’s just a matter of finding why you “lose power” at 50% indicated.
Can you post a log?
You were right , beginners mistake 
failsafe was set to high, now its ok. Thank you.
Could you tell me why after calm flying my battery is hot? could it be that ESC trying to take to much power from battery ?
Generally means you ARE trying to take too much from the battery.
Have a look at your current draw and compare it to your batteries specifications.