The AI system is completely separate from the vapor recovery system.
The vacuum lines attached to the manifolds operate control valves and replacing them with caps or plugs shouldn't have any affect on the idle unless one of the valves or hoses was leaking.
The only difference you will see if you remove the vapor recovery system is a slight reduction in fuel economy and maybe a little burning in your eyes when stopped on a hot day.
If you do remove the vapor recovery system, you should see about getting a rollover valve and fit it to the tank vent hose. Otherwise, you risk a fire if the bike falls over.
