Jisho.org lists 噌 as a Jinmeiyō kanji. By my understanding this means that the Kanji is permitted to be used for names, but is not considered commonly used for normal words.
But the word 味噌 (Miso) is still written with it all over the place. For example the Japanese Wikipedia entry for it.
What's going on here?
According to Japanese 戸籍法 (Family Register Act):
第五十条 子の名には、常用平易な文字を用いなければならない。
Article 50 (1) For the given name of a child, characters that are simple and in common use shall be used.
２ 常用平易な文字の範囲は、法務省令でこれを定める。
(2) The scope of characters that are simple and in common use shall be defined by Ordinance of the Ministry of Justice.
This is the legal basis of maintaining 人名用漢字 list. In other words, 人名用漢字 is a remedial pool for "characters that are simple and in common use" enough to be used in newborn names but not selected in 常用漢字 list. The fact conversely gives 人名用漢字 a certain connotation that it contains those secondly commonest kanji next to 常用漢字 (although 常用漢字 is maintained by MEXT and 人名用漢字 by Ministry of Justice). For example, in 2010, 129 characters were "promoted" into and 5 were "relegated" from 常用漢字.
噌 was introduced in the 2004 expansion, which is largely prepared with a purely frequency-based list, only removing some "obviously unsuitable for name" kanji (糞, 呪, 癌...) in public comments. Thus some kanji hardly has connection to given names. That said, 噌 is originally an onomatopoeic character in Chinese with no intrinsic meaning, which means there is nothing to prohibit you from using it as ateji as much as 味噌 is. A rare surname 一噌 exists as a Noh musician family.
By my understanding this means that the Kanji is permitted to be used for names, but is not considered commonly used for normal words.
This isn't really true. There are common words which use kanji which aren't Jouyo or even Jinmeiyou.
I don't think it should be unexpected when looking up words, just less common.
The jouyou kanji list regulates things like NHK broadcasts, government reports, textbooks, etc. It does not regulate Wikipedia or daily everyday writing. There are many kanji that are neither jouyou kanji nor jinmeiyou kanji, but are still used every day by Japanese people.
