I’m still very early in WaniKani, but I did some snooping around and it seems like 本日 (ほんじつ, right?） isn’t included in the program. When I looked it up it said it was a pretty common word, and I hear it used pretty often. Does anyone have an idea why it might not be included?
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Probably because they already have a lot of vocab that reinforces the ほん and じつ readings for those particular Kanji.
Plus I usually see it as 今日 anyway.
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WaniKani’s main purpose is to teach kanji, not vocabulary. When they select vocabulary to teach, the main purpose is to reinforce or teach new readings. 本日 doesn’t introduce any new readings and those readings are already taught a bunch, so it wouldn’t add much value.
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Plus, I’m forever gonna give the reading as にほん, so it’s good for my sanity to omit it. 
But in all seriousness, OP, 本日 is something you’ll usually see in fairly formal writing, like signs at shops and such. It’s not something you’ll typically use in conversation.
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本日、列車、乗車… there are plenty of common words out there that aren’t on WaniKani.
The intent of WK isn’t to give you a complete set of vocabulary to work with. Honestly, while 6000 words seems like a lot, it’s not that much.
From this source we have:
After children begin understanding words in the first year of life, their receptive vocabulary size increases rapidly. At age one, children recognize about 50 words; by age three, they recognize about 1,000 words; and by age five, they recognize at least 10,000 words (Shipley & McAfee, 2015)
Not sure on the original source for this one, but similar story with just how much vocabulary a native or fluent speaker knows:
So, not surprising that there are common words left out of a ~6000 word set.
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I had to read it again before replying since I was like, wait, 日本 is already on WK. 
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This comes up quickly in other vocab resources, but still nice to have useful vocab here just for extra practice (at least as much as they are willing to add).
I think they should add 勿 as a kanji just for the purpose of adding 勿体ない vocab. It’s an extremely common word and though Jisho says usually kana only, it’s probably closer to 50/50 from what I’ve heard. Plus they already have the radical 勿 so very simple.
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