To allay your suspicions:
1. The cooling water (not directly connected to the reactor!) intakes are at the aft (rear) end of the boat; they ran into something with the pointy end (bow).
2. The intakes are NOT on the bottom, but rather 'up the sides' quite aways - visualize viewing the sub from aft; the seawater intakes would be at about 4 o'clock and 8 o'clock on the stbd and port sides respectively.
3. The intakes are located as in 2 above precisely to avoid your scenario.
- Ex-submarine nuke RO (reactor operator)
Thanks for your service!
For the record... the "back end" of a 688 is "pointier" than the "part in the front".