Yes it can be related. I never found the cause and never fixed it. The freeze does not happen immediately and is very unpredictable (ie. quite hard to reproduce).
I also found in your savegame that you have some global tasks running that shouldn't be there ("Lib.Gen.RunScriptWhenFinished"), which indicates that a script is trying to run but something is stuck, somewhere...
Unfortunately, the debugging tools are very limited in X3. When a command runs on a ship, that starts a loop that you cannot just modify once it's in cache. However, destroying a ship removes all cache scripts attached.
Also, try to deactivate your antivirus
We never know. These things are nasty. After using Panda Antivirus (yeah) for more than a year, I realized a few months back that it was the cause of severe lags in some games, as well as some crash issues (Frostpunk wasn't launching at all). I doubt it comes from that, but you only need an antivirus when you're downloading weird torrents, or softwares that help you sleep with all the girls in your neighborhood.