You can update software, but you can't update hardware (as seen with Sky3DS). The reason why other carts were blocked was not the headers, it was the save chips - they were blacklisted on the basis of that chip they shared. DSTwo uses a different chip, hence it was spared. Its powerful processor wouldn't help one bit if the components were blacklisted.
It's really not as simple as you put it, but hey - at least they're innovators, not immitators. My guess is that they rushed out the product as fast as possible to get funding for future ventures - they were upstarters after all and made a cart that didn't require any software exploits, that's a big achievement that was probably costly to accomplish.
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Nonsense, the Nintendo DS wasn't updatable, sure, but the software changed over time, not to mention several system firmware revisions. Upgrades came along long before the DSi.