The stuff about the NDA I do find alarming. In order to write "secure" programs for the chip on the Yubikey, you must have an NDA with the manufacturer. In fact the open source pgpcard app for the Yubikey is different than what ships with the Yubikey because they can't open source the secure bits. Which is a bit upsetting. So uploading the open source version weakens your security.
That said, having my keys there still gives me much higher degree of security then an encrypted file on my computer. Malware may be able to get my pin, but not my keys.