WaniKani’s not bad for learning vocab, it’s just that it doesn’t teach a lot of it (~6k words), and vocabulary on here is primarily included to reinforce the kanji and teach different readings, which means not necessarily most common words, and a lot are kana only, as you mentioned.
If you’re looking for other places to learn vocab, there’s Torii SRS—core 10k, and Kitsun.io—lots of decks available, including a Genki deck actually.
It’s understandable not wanting to use lots of different systems though, and if you’re studying grammar elsewhere, you’ll be fine with WaniKani for now, so I wouldn’t stress. When you get around to reading, a lot of people find it helpful to use an SRS they can add to, too, so you can keep that in mind for the future. 