In my experience (and I have investigated this subject far more than I ever wanted to
), there are three major causes of corrupted saves that CTD on reloading: The first two I mentioned already: Touching your mod list while on patrol, and touching your mod list without rolling back SH3 Commander. The third is saving a game over the top of a previous save. That is, when you reuse a save name without first deleting the old save. Silent Hunter does not like that! If you have a save called "MySave", do not just select that name and save again. Either
delete MySave first and re-enter that name and then save, or call the next save something else.
But generally the result is a corrupt save that CTDs and can't be restored on loading. That's different than the mid-game CTDs that you are experiencing. Since your current career is messed up anyway, I think the fastest way to get back to a game that you can enjoy reliably would be a complete re-install.
The snapshot function is found on the Tasks menu in JSGME. The JSGME User Guide explains what it does and how to use it. It will tell you if you have a corrupt copy of the game and/or one or more mods. But it won't fix the problem. You will still have to re-install the corrupt software. But if the problem is in a mod or two, you will only have to re-install those, not the whole enchilada.
I have found that most of the conditions which the GWX manual lists as causing problems can not be reproduced in practice. I have saved submerged, in the middle of a depth charge attack, under a convoy, within 50 km of a port, and reloaded that save with no problems. But if you want to be ultra-safe, follow the GWX recommendations. YMMV.