It's still pretty silly, considering the absolute value of the savings.
My personal favorite along these lines is the way that a single building might have 2-3 floors of the same kind of restaurant (say, yakitori), but the one place that is 5 yen cheaper per item will have a line out the door, while the others are half-empty.
Is this a cultural thing? I've never been to Japan so I'm kind of flying blind here but I'd assign that 5 yen as a convenience cost and happily pay that price to avoid the long line. I have a hard time thinking the Japanese people place no value on their time whatsoever...
Usually it's an up to 150 yen onigiri for 100 yen, so of course they're going to get excited.
Edit: It looks like it is/was an up to 160 yen onigiri for 100 yen! That's a 37.5% discount! [1]
[1] http://seven-eleven-mania-blog.jp/gohankei/5617/