They both have limited write cycles.
The beauty of flash media, be it USB or SD, is that it's removable.
Simply backup the entire card/USB and transfer it to a new/larger one.
Flash media life expectancy is consoles is several years.
Like Smiley said, professional photographers shoot hundreds of photos a day.
It'll be years if not a decade or 2 before it reaches it limit.
tl;dr, What Nintendo said is pretty much nonsense.
Removable media is user friendly, as soon as you start to notice performance drops/odd errors, you can back everything up and copy it to a new card/USB drive.
Edit: you barely put write cycles on the media if you only store games on it.
Same goes for saved games.
Yes you can argue saved games write more to the media but even that isn't enough to make the media die within a short span.