Recently it's seemed like (very roughly) half the Little Free Libraries I see aren't in OSM.

I sometimes edit OSM, so I'm wondering whether any public bookshelf omissions are intentional, and adding the shelves would be unwelcome by the people running them.

I see OSM as a mapping application. It is in the real world, publicly visible for a long period of time, and there is no law preventing sharing the information (like military stuff) it can be in the mapping application (decide what is relevant enough is another story).

I would not include the wishes of the people into it, because there are various groups that might have strange ideas (dunno, like only churches of some type should be shown; or no shops of a certain kind because it hurts my feelings, etc.).

I personally would not like any edits that advances the wishes of "any" group of people (like removing features). I do not like all things that exists on maps, but I will not remove them because of my feelings.

The few places I have seen book nooks like this, they end filled up with religious literature which is usually not the intent of the person who started it.