The emails UI disables your ability to manage notifications for all followed channels, but you can still manage per-channel notifications by clicking the dropdown arrow on the follow button of whatever channel you want to modify notifications for.
As for you getting only some notifications, that’s probably because push notifications have always been hit or miss. Twitch also recently disabled follow notifications of streams it thought you don’t watch: http://blog.twitch.tv/2016/01/fewer-notifications/
As for submitting feedback or asking non-developer questions, this is not the right place to do so. You can email feedback to feedback [at] twitch.tv, submit ideas to the Twitch UserVoice, submit a bug report, or ask for Twitch assistance via their helpdesk.