Saving at least
50 km from the nearest ship, land or other object is probably the "safest" thing to do to avoid a crash to desktop (ctd). Avoid saving while submerged as this will probably lead to a ctd as well. Don't use the crew config screen (the one with the "surface attack" buttons, etc.) in the crew management screen (F7) as this will likely lead to a ctd; move crew around manually. If you're using a "Supermod" (ie. GWX) don't enable or disable mods while out at sea as this can cause instability too. Finally, save at least 50 km from the last ship that you sank. If you save any closer the game may respawn that ship & you won't get any credit for sinking it again. The game will credit you for sinking it the first time though
Hope some of this information helps. Unfortunately there is no one "magic bullet" for the game's save game issues. You can do all the right things & still get a corrupt save...
P.S. It's all about money. Ubi forced the development team to get the game out before it was really ready.