It would be great if when you create a web map there is an option for "Show in Collector". If this is checked then your org users will see it in their collector apps if it is shared to a group they are a member of. If it is unchecked, they won't.
The main use case for this is if you are using groups for user access control. You might want to have multiple maps shared to a single group of users, but only want some of them to show up in collector to prevent confusion.