The Miata is a "halo" car that shows off their engineering and car-enthusiast spirit. It doesn't have to be a half million dollar car to bring attention to the brand regardless of sales volumes - the Miata has been playing that role for Mazda for a long, long time. They let people know that they "get it."
What does Honda have on it's floor that gets car nuts excited? The Si? I suppose, but it's still a FWD car that is far from the stripped down RWD lightweight that the Miata is. Right now Honda cares a lot more about CR-Vs than anything with RWD or a manual trans. It's all about business. Glad Soichiro isn't around to see what the current product line is. He sold normal cars to make money to build other really cool stuff like outrageous motorcycles and neato cars.