You're kind of missing the point of online video on-demand. Linear television has very limited time schedules and very limited bandwidth to work with, and advertisers can more freely pick and choose precisely when their ads air. Moreover, when one thing airs, it directly takes the place of something else - if one episode of Class of 3000 airs at 7:00, it's directly usurping an opportunity for something like My Gym Partner's A Monkey to air. Therefore, making the absolute most out of the limited time available is the highest priority, even if that were to mean airing the same episode of "My Gym Partner's A Monkey" all day long.
Online, however, is much less restrictive - even if, in theory, one certain episode of My Gym Partner was given the highest chance to succeed in every single timeslot throughout the day, online that episode only needs to be uploaded once, and is limited only by the amount of bandwidth CN chooses to afford it (which is potentially limitless, unlike TV).
So even if 90% of all visitors just wanted to watch My Gym Partner, CN loses very little by adding as many other shows as possible to their streaming service to catch that other 10%, and since advertisers generally pay to advertise on the whole service for all viewers, rather than dividing their time into specific shows, CN has almost nothing to lose and everything to gain by appealing to the minorities who'd rather go for Cow and Chicken, unlike linear TV where airing an episode of Cow and Chicken means gaining some 10% they might not have had, but losing some 90% they otherwise would have had by airing My Gym Partner.
Put more simply - it's not that because something is still available on CN Video means there are enough people to watch it on TV, but rather that, unlike TV, CN can afford to serve the minorities' interests online while they can't on TV. In fact, in some ways, the less popular something is (within reason), the less bandwidth it uses, and therefore the less expensive it is. And because advertisers are paying for the whole package moreso than for each individual show, CN only really has to worry about turning a profit off the whole service rather than off each individual show.
In other words, consider it a bonus that you get extra shows on CN Video that you don't get on CN, rather than the other way around.
