The split between on’yomi/kun’yomi on Wanikani’s kanji reviews is something like ~1700 on’yomi, ~300 kun’yomi. The idea is that you hopefully learn whichever reading is more useful to know when you see the kanji in an unfamiliar word.
I’d recommend using [Userscript] WaniKani Katakana Madness, because with it, you’ll passively learn whether each kanji reading is on/kun based on whether your answer appears as ひらがな or カタカナ. You’ll also get more exposure to katakana, making it easier to read at a glance 