Hi Craig,the /who command is supported by your IRCd, so anope modules shouldn`t be able to fix your wishes Sorry
In general operators see all users in a who listing no matter if on the same channel or not and no matter if the user has +i or not. Users not oper'd would not see the bots in the who listing since the bot is +i unless in the same channel. I don't think there is a way to hide the bots from operators.
Without knowing anything about the IRCd you are using it would be hard to assist any further on the issue.