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I don't have any special knowledge about how submarines get controlled, so this is mostly speculation.

I expect that the actual controls are fine.  There seem to be the necessary degrees of freedom, and as you say, people are already familiar with the interface.  In that sense I don't see anything wrong with it.

However, when I heard about it, my first reaction was that it might be irresponsible due to reliability.  A consumer game controller like this is going to be optimized for high flashiness and low price.  Reliability was likely not a major design consideration, as long as it doesn't fail so often as to be considered junk by the market.

If the controller stopped working when you're playing a game, you'd be annoyed and be out $50.  You'd shake it off and get a replacement, maybe a different brand this time.  The cost of failure is relatively low.  If you suddenly can't control the submarine you're in 2 miles under the ocean, you're going to end up dead.  The cost of failure is high.

There is a reason military and other high-rel electronics cost more than the equivalent consumer versions.  There are rules for how much every part must be derated for temperature, voltage, and other parameters.  You have to do formal testing to show that the product survives in dry heat, damp heat, cold, vibration, electrostatic discharge, etc.  These things cost real money and delay the design cycle.  I've been thru tests like that with industrial products.  The tests usually find something that requires the design to be tweaked.  All that adds cost, but makes the product more reliable.

Especially for something that goes near the ocean, I'd want contact mating surfaces gold plated.  Corrosion, even just due to normal air in a marine environment, is something you have to consider.  I'd also want to know that the design passed vibration tests.  That's not because a submarine like that vibrates a lot, but because it makes the unit less susceptible to normal dings and small accidents.  If you drop your game controller on a concrete floor and it breaks, you'd probably blame yourself.  If it got accidentally banged (that's going to happen) and breaks in a submarine, it doesn't matter who you blame, you're dead.

One way I could see the use of a price-optimized game controller be acceptable is if there were at least two spares on board that are regularly checked to make sure they are ready to use.  Now you need three failures in three independent units in the space of a few hours before there is a serious problem.  That's a much lower risk.