I had the same problem after months of rock solid running. It turned out not to have anything to do with my mod load errors. Looks like you've probably experimented with quite a few mods, trading them in and out as you find what works for you. Somewhere along there you could have uninstalled in a different order than you installed. This can make a hybrid frankenmod which can contain the seeds of its own destruction. Then you reinstall it causing.....CRASH!!! Either that or it's cosmic rays, who cares?????
You'll probably never know what the problem is.
But you can still fix it. I tried using 42, the answer to life, death, the universe and everything, but it didn't work with Silent Hunter 4. So it's time to try what looks draconian and too complicated, but what can actually be done in about ten minutes.
1. Move your MODS folder to your desktop for safekeeping.
2. Uninstall
Silent Hunter 4 using the control panel. You could try using the repair option there, but I like to be absolutely sure I know what's happening so bear with me.
3. During the uninstall process you will be given the option to save your save-games. Do it or you're starting all over. Don't want that.
4. Reinstall Silent Hunter 4 and apply patch 1.3.
5. When you uninstalled, since JSGME lives in the main program directory, it is gone. Reinstall JSGME from the SUBSIM website.
6. Run JSGME once to make a MODS folder and exit without installing anything. There's nothing to install at this point anyway!
7. Move your MODS folder from your desktop back into your new main folder. It will overwrite your blank MODS folder created by JSGME.
8. Run JSGME, installing all your mods in the correct order.
9. You're back in business. Play Silent Hunter 4 and go into therapy so you don't torture yourself for the rest of your life speculating about what really was wrong when you had all those CTDs.
10. Live happily ever after.
Well, there you go chum! Other possible remedies, like drinking to excess, kicking your dog (borrowing neighbor's dog if necessary), cursing, eating Mexican food of dubious origins, etc, may bring temporary relief, but for a true cure advanced and radical surgery is the only answer! (I've been watching altogether too much Strong Bad)