I have found the cause of the problem. It was top front right side engine mounting. The hydraulic one.
I found it by locating a microphone and run a cable to the cabin and record it with laptop. I have placed the microphone into several points which i suspect and ultimately end up right at the engine mounting.
What puzzled me is thaf mounting is still look fine from outside. The only thing i can see is the remaining gap is only 3-4mm. Also i found a TSB for Honda civic for other car which suggesting engine mouting replacement. And the cause of the problem is cavitating engine mount. Then i decided to give it a try. After installing new engine mount. The noise disappears.
Before finding the problem, i did try tightening the subframe to the spec after loosing it while under the load. And that didnt help.