Obligatory Sheldon Cooper reference.
I bet that if the Japanese tried the same trick, Americans wouldn’t have been fooled.
To answer the OP, the use of an upside-down flag to indicate distress is pretty rare in modern times. Mostly because it
- isn’t very well recognized, and
- isn’t much needed.
Many (most?) flags are symmetrical, or nearly so, and unlikely to be recognized as a sign of distress. And you’d have to be quite close to even see a flag, and notice it – ships in distress are usually more isolated than that.
And in modern times, there are so many other, easier, unambiguous forms of communication available to people than the upside-down flag. Everything from a bullhorn or sending SOS via a flashlight if there’s a ship within sight, to radio, cellphone, signal flags, even sending SOS via ships radar or sonar. Many of these allow speech communication, to give more specific details of the ‘distress’ and what aid is needed.
So there is very little use for this old tradition in modern times.
If St Patrick’s cross were simply superimposed over St Andrew’s, with the latter sufficiently wide to show that was a saltire, not just fimbriation, it would appear that Ireland was being given superiority. Superimposing Andrew’s over Patrick’s would give the opposite impression – that Scotland was being given superiority – and would also break the heraldic colour-on-colour rule. As it is, on two arms of the saltire the red portion is closer to the top of the strip, but on the other two it’s closer to the bottom.
It was also oddly enough used in two different Japanese video games, which makes me think maybe over in Japan they assume it’s a lot more common in the US than it actually is.
In Resident Evil 2 the Police Station press room American flag is upside down, while in Metal Gear Solid 2 the place where the US President was going to give a speech also has its flag upside down, presumably to illustrate the great distress of zombie apocalypse in the former and terrorist takeover in the latter.