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From my understanding, the motors and RC receivers are not waterproof. Thus, the LEGO submarine from Sariel's LEGO® Workshop rust after sometime.

So, is there any way to make the motors and RC receivers water-proof, so that it can be used as a submarine?

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The method they used to secure the battery/controller was to wrap it in a sealed plastic bag, something similar to this could be done for the motors. It would be more difficult since you would need a water tight bearing for the rotating shaft to exit the sealed bag. These bearings are complicated and will still always allows some small amount of leakage.

An option to help prevent water leakage would be to fill the motor with a non-conducting fluid to displace any inflowing water, something like mineral oil. I'm not going to try this with any of my motors, but it should work. There is history of using mineral oil for electronics to aid in heat transfer (used by some extreme CPU over clockers) it is non corrosive and non conductive and will not rust the metallic components.

As an alternate just letting water in seemed to work for a while, you could prolong motor life, by ensuring the internals were thoroughly dried after removing them from the water. This would most likely involve opening the housing and a dry air flush. This would slow the rusting, which is much faster when water is combined with exposure to the oxygen present in air.

EDIT

Another method that could be used with actual Lego parts, use the Lego magnets to couple two shafts rotation together on either side of the plastic bag around the motor, this should have zero leakage. There would be an upper limit on the torque possible before the magnets would slip and it would potentially cause wear onto the plastic bag if there is contact with the moving parts.

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The only option is to seal the electronic parts away in a waterproof container, like the plastic bag used in Sariel's video contained in the question, or in a clear plastic water pitcher, like in this video. The tricky part is then providing waterproof seals for the propulsion shafts that need to penetrate the hull. The different approaches tried can be seen beginning at the 1:53 mark and finishes at 3:20 with the application of a small, non-LEGO O-ring, sticky foam tape and a metal washer on the other side: enter image description here

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