I am looking at CodeMirror help and registerHelper is described as
CodeMirror.registerHelper(type: string, name: string, value: helper)
Registers a helper value with the givennamein the given namespace (type). This is used to define functionality that may be looked up by mode. ...
This does not explain what the value is, when is it called (it seems to be a function), or why getHelpers accepts a position.
Is helper similar to a mode, but providing non-visual annotations (for code lookups)?
It's just a value -- any value. How it will be used depends on the type of helper. For "hint", it'll be a function providing completions at a given point in a document, for "hintWords", it'll be an array of strings that form possible completions, for "wordChars", it is a regular expression describing the characters that count as word characters for a mode, and so on.