My experience with Nitrokey is different. I trust Yubico for my threat model, I just don't trust Nitrokey at all. They seem to have more products than employees and in my experience they have a history of advertising/selling features they don't have.
They have 1. Nitrokey 2. NitroPhone 3. NitroTablet 4. NitroPad 5. NitroPC 6. NextBox 7. NitroWall 8. NetHSM which look like very different products. On top of this, they have consulting services and NitroChat (not clear to me if it is just a branded Matrix instance) and "Android FIDO SDK" (which for some reason points to https://hwsecurity.dev/, which doesn't exactly seem to be a Nitrokey product). That seems like a lot for 14-20 employees.
But then my experience was with the Nitrokey 3 NFC. They advertised all the main features that Yubikey had and accepted pre-orders. They claimed that the software was ready, in Rust and open source (!), and that it would just take a few months for the hardware. It took 2 years, and when I finally received my Nitrokey, none of the software was ready (it had just one feature, maybe FIDO?).
Finally, it is great that it is open source, but the fact that it is flashable does not sound like a security feature to me: doesn't it mean that an attacker could flash a malicious firmware on it from a compromised computer?
What it comes down to is that YubiKeys have better integration but Nitrokeys are more fun if you want to hack on them, and it's not really a matter of security. Note that smart cards in general can be used for the same purposes, e.g. Java Cards. USB keys do not require you to carry around a card reader.
Isn't there a difference between your compromised laptop being able to reflash your Nitrokey and your compromised laptop not being able to reflash your Yubikey, though?
> Them having less than 20 employees makes sense, it's a niche market.
Maybe, but they sell 8 different hardware products. Have you ever been involved in a hardware product? I have, and it feels like they must not put a lot of resources on them. Which is kind of proven in my experience with the fact that my Nitrokey arrived 2 years after I ordered it and by then, only a fraction of the software had been written.