Reputation for per-site metas is not shown in the 'Your Communities' list in the sidebar menu of the Stack Exchange iOS app (anymore – it used to work before).
App development is currently frozen, but this looks like a bug solely caused by the Stack Exchange API. I suspect the app uses the
/me/associated API method, and it doesn't seem to return data about meta sites anymore. You can test this with this call (remember to click the 'Get Token' button); compare that to the result when you leave the
types parameter empty.