Despite this affecting only FIDO and barely any Yubikeys are being used for that, it’s important to keep in mind that exploits and attacks get worse over time. For now it’s just FIDO and requires complex hardware and practically destroying the key. I wouldn’t be surprised if this exploit is just the beginning.
Really depends what you’re chasing. If you want overall performance then 256GB is the better choice. It’s quite a bit faster than 128GB in terms of actual physical chip performance. There are diminishing returns in performance once you go above 256GB.