There are several things worth mentioning.
1) Jisho is compiled from freely available databases that anyone can contribute to. They don't create the vast majority of data you see here. If you see an issue you want to address in the data from one of those resources, you can use the about page to find out which one it is and try to send a correction via whatever method might be needed. I'm not saying you have to, just wanted to establish what Jisho's relationship to the data is.
谷's page does list や, though in the Japanese name reading section. This is also referred to as nanori in Japanese. It's not prominently visible on the page though, I suppose
河童's reading is exceptional. It's basically a drastic shortening of 河にすむ童 (かわにすむわっぱ). Readings born of sound changes, ateji (using kanji only for their sound), or other quirks of history, typically are not listed as official readings in any resources. You won't find ぱ as a reading for 童 in a monolingual kanji dictionary either.
I hate that you can't edit here. Numbering got screwed up lol.
Unlisted Kanji readings
I've noted several kanji where, in everyday use, the reading for the Kanji is not listed as either an ON reading or a KUN reading in any of the common Kanji dictionaries. For example; in the following words 四ツ谷 (yotsuya よつや) and 市ヶ谷 (ichigaya いちがや) the kanji 谷 is pronounced や. I don't see や listed as a reading for 谷. The same for the word 河童 (kappa かっぱ). I don't find either ぱ or は listed as reading for this Kanji. Is there something special going on or, am I not using the kanji dictionaries correctly?