So I’ve seen a couple of people mention that wanikani gives you the ability to (mostly ) accurately guess the reading of an unknown kanji. How does this work and is it something I should worry about on the lower levels of wanikani?
It’s mostly from radicals. You can see the same radical in many different kanji, and then guess what a new kanji means by the radicals in it. Doesn’t always work. 
As mentioned above, it’s by recognizing some radicals. You won’t necessarily recognize all of them but few of them should be enough, sometimes even one is fine if the Kanji isn’t complicated.
Once you spotted a radical or more, you use something like https://jisho.org/. With the “Radicals” feature you will have a list of Kanji that use the selected radicals and you will be able to find the Kanji that you were looking for.
It does take some time to find a Kanji but I think it’s still worth it. Obviously, the more you practice the less time you are gonna spend to find a Kanji 
You can take advantage of the etymology of the sinograms (aka. kanji) - it relies on the phono-semantic principles :
<< Kanji are very different from English compound nouns, in which both the words are pronounced equally.
For example, kanji 飯 /han/ ‘rice’ can be divided into the left and right
components: 食 /shoku/ ‘to eat’ and反 /han/ ‘to rebel’.
The right side of kanji 反 /han/ ‘to rebel’ gets attached to various characters and contributes its phonetic shape to compound characters. These compound characters have the same pronunciation as反 /han/, for example:
飯 /han/ ‘rice’, 版 /han/ ‘print’, 坂 /han/ ‘slope’, 販 /han/ ‘sale’ and 板 /han/.
This is a clear example of how kanji compounds with the same or similar pronunciations usually include the same component. It is called a phonetic component because it provides a clue to the pronunciation. >>
Extract from Phonetic Components in Japanese Characters Thesis
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Basically, it’s because 工 江 攻 功 項 紅 have the same reading, and 祖 租 阻 粗 have the same reading, and I think you get the idea.
Edit: Just edit to add that 反 is a great example
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This is probably the answer you want @kennypow.
To help you visualize this while you are using wanikani you can try the script below that shows you the meaning (semantic) part and pronunciation (phonetic) part of the kanji during lessons. There are exceptions but it will definitely help you on most kanji.
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