I'm having the same issue, so I'll post what I can in hope to give more info to solve this problem.
I've had this freeze that requires to kill DCS in the task manager on different servers in multiplayer and in solo on different missions, every time with the same loadout of 3 fuel tanks 4 Aim7M and 2 Aim9M, and I use waypoints and TACAN to navigate. I ran multiple tests and every time the game freeze to death after about the same time, roughly 20 minutes. As for the others, nothing in the log file to exploit, the last entry is from 10 minutes before the freeze, I attached log files and a track file of a flight that ended up in a freeze.
Somehow, I tried the hot start instant action mission and wasn't able to reproduce the freeze after 40 minutes of flying the same way, with waypoints and a Tacan, but this time no loadout.
I tried a cleanup of DCS and a repair, deleting the metashaders folders, and no change, it keeps freezing in the hornet.
My specs are the following:
Win10 Home 64bit, Intel I5-4690K, GeForce 1060 6GB, 500GB SSD, 16GB DDR4 RAM, Edtracker, Logitech X56, Logitech Rudder pedals. Logs.zip Patrouilleur_du_FAIL_v89_experimental-20180602-005817.trk