Applause sold ~150k in Japan. Still bigger than any Katy single. And let's not forget BTW remains the best selling western single in Japan of this century (1.3M copies).
Yeah Gaga had a nice run. But not getting any Japanese certifications is not a big deal, hardly any foreign artist does. In the end PRISM still sold three times as much as BEYONCÉ in Japan, so there are more embarrassing examples.
296 Lady Gaga The Fame
815 Tony Bennett & Lady Gaga Cheek to Cheek (Deluxe Version)
995 Lady Gaga ARTPOP
1203 Lady Gaga The Fame Monster (Deluxe Version)
1352 Lady Gaga Born This Way (Bonus Track Version)