Heya.
The TM 1.6.2 patch that you're using has tougher damage modelling. If you want to go back to the way it was in 1.6 just remove the 1.6.2 patch and TM 1.6 with your JSGME.
Next, go into your mods folder in your game directory and into the 1.6.2 TM patch file. Delete the /Data/Zones.cfg file.
Lastly, re-enable the 1.6 and 1.6.2 patch mods in your JSGME.
Now you're back to the easier sinking!
Note:
I did this myself. While I liked the idea of better damage modelling, I experienced a case of having to use 9 torpedoes on a Light Cruiser before it sank. That's a little too hardcore for me.