With respects to the IMU and stuff I think that you can use a 9 DOF for full 3D orientation because the rotation in Z axis drifts (like the others angles) because of the error integration in time, so with a 9 does you can use a complementary o Kalman filter to keep data stable and then applied a PID or something.

Nice  Work! I always wonder if I can use ruthless motors like ds2830 in water without any protection against water, and if its applied to salt water too Do you know if it's possible?

Would be interesting to see if optical fiber is closer to neutrally buoyant.. You can get optical fiber converters for about $25 each, or a pair of BiDi (uses a single fiber for both directions) converters for about $75.  The latter are good for about 12 miles of fiber length.

As for the sealed container concerns, install an air pressure relief valve.  It will never open unless the inside pressure gets up to whatever value you pick.  The common ones are rated around 130-160psi.  Although if your LIPOs are venting you have much bigger issues.

Lastly, you should be putting the majority of your mass (batteries) as low as you can for more stability.  Commercial craft often sling them underneath in separate tubes.

I've been working on a ROV myself in my free time and made some similar decisions. Would love to see more info on this build, might help me fill in some blanks on mine.

Particularly curious about the watertight compartment, I can't quite understand from the pictures how it works. What are the bolts going into?

The hull of ROV is PVC, which has an aluminum flange that is permanently attached to the PVC with a bead of silicon and screws. That piece of aluminum has 8 tapped holes to allow the lexan plate to attach to it. The seal between the aluminum and lexan is a large O-ring that gets squeezed down as the bolts are attached. I will attach some pictures as well in the details.