I can think of at least three reasons for publishers to want to give people incentives to buy physical copies off the top of my head, I'm sure there's plenty more.
Selling digital copies means they'll be ripped and posted online and destroy physical sales.
People are more likely to complete their collection if they have physical copies because of material attachments.
It keeps relationships with bookstores open which they need to promote and sell the magazine.
1) Piracy was not born with Kindle, it was there since before that, scanners are meant for that, Japanese publishers started to make digital edition available just very recently, there are mangas that even don't have any, it doesn't stop Manga Editors to rip it and will never stop.
2) Material attachment doesn't exist in Japan, there are plenty of manga cafe where you can go, pay a small fee and read whatever you want without cluttering your room with books. There was another service, a rental service if I'm not mistaken, I will have to ask my Japanese friend on Twitter. If I were in Japan, I would have no reason to buy mangas directly.
3) Heh, maybe it is a fair reason for small publishers, but Shueisha... The bookstores need more Shueisha than Shueisha needs bookstores. XD