However, my casual judge-by-the-contents-of-the-rental-rack guess is that the newest megahits are over ten years old at this point. (Before Bleach and Naruto got big in America they were big in Japan. Big like "qualify as industries unto themselves" big.) Both of them are actually animated in Korea, incidentally. (And, oddly enough, both are quite "high tech" in terms of animation techniques. It is sort of the series' aesthetic.)
Incidentally, Youtube isn't the enemy of Japanese DVD sales. Rentals are. Japan does distribution really freaking well: there are about three or four companies with reach as good as Netflixes, plus plenty rental chains stocked with up-to-the-minute DVD releases. Here's the math: $200 for a 4 DVD boxed set or $8 to rent them all. Not hard to figure which one wins out. (Or you could go rent a big screen TV and a comfy chair at an Internet cafe for $2 to $4 an hour and get the DVDs loaned to you for free.)
That said, getting a hit series is not really an easy thing for authors (mangakas). They work about 14 hours everyday and have to produce 19 pages of content every week. The gruelling workload takes a toll on a lot of mangaka's health, forcing the series into a hiatus, which further reduces their chance of becoming hits.
Youtube might not be much of a problem within Japan, but it certainly hurts the overseas profits. Also Japanese studios are incredibly lax when it comes to enforcing copyrights. They usually let fansubbers and scanlation groups get away with pirating weekly chapter releases in the hopes that this would encourage people into buying the volume releases when they are available.
To say nothing of Gundam...
And often even when something does become a hit, it creates its own problems: for example, from what I heard, the author of Death Note planned to end the story at what eventually became the halfway point. Instead his publishers told him that it had become so popular that they wanted him to make more of it, and so he dragged it on for a whole bunch more chapters.
There's also the fact that a huge number--probably the majority--of authors don't seem to care too much about making huge hits. Just look at the sheer volume of doujin productions: nobody there ever intends to even make enough money to pay for their own time, yet there's probably more doujin manga than professionally published stuff.
It's funny... There was a minor controversy a few years ago when someone discovered that several Naruto fight sequences were actually traced off of other sources, including the Cowboy Bebop movie. I wonder whose idea that was -- the main studio or the outsourced one?