This is an interesting description of a problem that you don't normally see with surface ships. On most traditional naval ship designs, shafts are connected to the power plant. In most cases on Navy ships, these are either gas turbines or nuclear (carriers). The shafts pass through the hull, and connect with the propeller blades or screws.
These shafts transmit power from the engines through to the screws (propellers) by spinning. The faster they spin, the faster the ship goes through the water. Some ships also have variable-pitched propeller blades that can maintain a certain shaft rotation, but can increase or decrease the speed based on the angle of the prop blade.
The propeller shafts passing through the hull is not a trivial design. The seals have two primary functions: 1) is to allow the shaft to spin freely; and 2) is to maintain enough watertight integrity to prevent seawater from entering in too large amounts. As some alluded to in their posts, it is inevitable that some seawater will enter. Any water that enters will be directed to the bilge areas and will be pumped overboard. Kind of a sump pump for your home, except it's on a ship.
The Navy (and its contractors) have been building ships with shaft seals for a long time. I can only imagine that this hull design called for something more radical and unproven. Hopefully, it's nothing that will sidetrack the ship for too long.
If propulsion is electric generated, I’m surprised they didn’t do an APOD design.