I actually have a theory on those bracelets and the high heels, on a planet that exceeds our own gravity by 950 times, and Samus being able to jump up to 40 meters in those conditions, what do you think her strength would be on earth? those bracelets are not for decoration, their weights, without them Samus could kill anyone that she fights in the smash tournament, thus she wears the bracelets to slow her punches to at least a semi non-lethal level; and the boots to keep herself from flying into low orbit.
Considering I've seen even more impractical shoes being worn in fights (Aya Shameimaru's almost stilt-like sandals with the half-foot-high 'heels' in the middle come to mind) the issue with the heels sounds more like 'They changed it, now it sucks', than 'How can she fight in those?'
On another note, the sneakers (second from the left) look like something out of Inticreates' (Megaman Zero or ZX) designs from what I see.
First off, what Aya wears are a variation of Geta, traditional Japanese footwear. The single tooth variation is even referred to as Tengu Geta. They were often used with traditional clothing or to keep the feet dry. Since combat in Touhou happens in midair, the choice of footwear is not all that important and Aya is considered very old (roughly 1000 years) and Tengu are depicted as a very traditional sort, hence why her wearing Geta is actually not that strange in context.
Here's another thing that doesn't work in context of your argument. High heels force the person to alter their stance to something not intended for fast, dynamic movement. Tengu Geta do not change your stance, but they do reduce the area of your feet on the ground considerably, which means you have to much more precise with your movement to not lose your balance. This is why a popular and universely understood means to show that someone is a superbly good fighter by having them fight while wearing Tengu Geta, without breaking the tooth.
I'd say they were a bit more puzzling in Other M, where her Power and Zero Suit had completely different heels.
In this new Smash Bros., she can no longer switch her form during matches. It would make sense for her to beef up her Zero Suit with a gadget or two (seeing how it was never meant for combat). Her shoes do in fact look like something external (keeping her actual Zero Suit sole rather flat), not something she actually wears under her Power Suit.
Still, I would've gone for jet packs, or big boots that turn into drills Fourze-style. Or even just a more sturdy or visually pleasing design.