Check a parts fiche. The top breather hose goes to an oil separator thing in and under the filter housing airbox, this lets the vented gas/smoke/whatever get sent into the engine and burnt with most of the oil and water included separated out and drained. There's a sheet metal bit spotwelded into the bottom of the filter housing where a plastic foam separator element would go, also should be a cover for that and a round thing screwed on under the filter housing: the tubes connect there.
There are around 7 parts for the whole unit, some inside the airbox and some outside. Some are NLA.
It is common to just get a longer piece of hose and just route it so the engine vents behind the engine by the swingarm pivot. Filters are available as well that look like miniature carb pods if you're afraid of getting crud sucked into the engine.
If you have the parts, you should use the separator and reduce pollution. If it's been removed then probably don't worry about it.
I haven't had an air inlet manifold for maybe 40 years (pods) but I don't remember a drain. This manifold is the rubber bit with a big hole to the airbox and four smaller holes to the carbs? If it does have a drain nipple, it should get a pinched drain tube - these let water (fuel?) drip out but don't let air in. That manifold has filtered air. I think the amount of dirt that could get in a small hose nipple is not worth worrying about and you can just leave it open. Plugging it would not be so good in my opinion, it's there to drain something.
