Learning vocab with wanikani or 1000 most common japanese words?

Correct. WaniKani organizes kanji based in part on how simple or complex the kanji is. That means you’ll see some simple kanji used in uncommon words long before you’ll encounter some more complex kanji that show up everywhere. For example, (おれ) isn’t taught until level 44, but if you get into reading a lot (such as by joining the Absolute Beginner Book Club here on the forums), you’ll probably unintentionally learn it through repetition long before you reach level 44.

This will be a little more depending on one’s individual learning style, but yet, this is my recommendation to at least try out and see how it goes.

Learning the most common words will make it easier for you to start reading native material if you haven’t already.

This is definitely what I would recommend. I tried learning the most common words without furigana on the front of the card, and after two years I failed to learn much. I picked up a lot more words through watching anime. When I started reading material (with furigana), learning words became a lot easier for me.