Is it possible? Yes. You'd need new hardware as the bootrom is physically inside the SoC.
And for most electronics hardware repair nowadays, it'd be more economical for them to just replace the whole motherboard rather than having the technicians de-solder and re-solder a BGA chip.
As the exploit was only revealed recently, it's not possible for them to have already produced a new motherboard revision and shipped it to repair centers. (And mostly like will still be present in the unreleased N2DS XL as well).
Would Nintendo invest in a 3DS board revision at all? Probably, but not in the short term and most likely not at all. Right now, their production hands are tied for the Switch. Later the 3DS may not be profitable enough to justify a new revision at all. (They'd have to order a new chip design from the fab and those have to be in bulks. The remaining sales may not be enough).