It seems technically doable and would have some benefits

1) Lesser impact on deep sea ecosystems. No human trace left behind.

Disposable loads of iron or concrete will remain forever in the bottom. If we use salt or sand instead the impact on fragile deep sea ecosystems seems reduced. The organisms there are adapted naturally to deal with very salty water. The sand or salt ballast could be released gradually over a bigger surface reducing even more the impact over a particular spot or colony

2) Improved economics?

To dump valuable iron made with valuable energy into the sea seems a suboptimal solution. Substitute it with some common by products that are yet in the area and don't need to be transported from a mine far away could save some money probably. Containers of ballast would be fully recyclable also.

3) Extra safety.

If your load weight gets stuck by a net you are trapped in the bottom forever, With a ballast of sand or salt you have the extra possibility of open a few escape valves and let the concentrated salt go away. You can also release part of the weight much more gradually. After a while the submarine would tend to float and ascend automatically even if the energy supply would have been entirely lost in an accident.

Having the machine on the surface (or closer to the surface) would save millions and would made a big difference on humanitary and economical aspects of the rescue operation. A damaged submarine can be still repaired. Building another would be much more expensive.

Dunno about the possible negative aspects, more volume required for example, but would deserve thinking about it a little more.