According to icv2.com, manga sales have fallen 10% in the last year: "After years of growth, manga sales actually contracted in 2008, dropping from $210 million in 2007 to $175 million (roughly 2005 numbers), with larger declines in the bookstores than in the comic shops." That's quite a drop from the highs of a few years ago. The site goes on to speculate that the drop of anime series on the Cartoon Network, coupled with a rise in interest of the Twilight series kept new manga titles off readers' radar (and perhaps out of their pocketbooks).
I believe that the market has been saturated and is now leveling off. This is not a death-knell for manga in bookstores though I can imagine that publishers and stores are leery of their sales.
When I attended the NYComicon this past weekend, I heard from a Vertical publisher that they had cut back on the number of titles they are putting out this year because of shaky financial backing. I would imagine that their high-quality books (which are lovely) will also not be in demand as much as the inexpensive omnibus editions that other publishers are putting out.
But, why, may you ask did comics do so well in 2008? Two words: Watchmen and Batman.