In actual fact, WaniKani is missing 173 of the Joyo kanji - it also teaches 57 kanji that are jinmeyo, not joyo. And yeah, questions have indeed been raised as to why you’d get so close but not go all the way.
But the fact of the matter is, the remaining 173 joyo kanji are used so rarely in real life that odds are you’d never encounter them. It’s a case of diminishing returns, basically - you’d put a whole bunch of effort into learning the last few kanji for comparatively little benefit. Why learn, to pick a random example, 麓, which is used in precisely one word, namely 麓 (ふもと), when you could instead learn 瓜, which is used in many words?