The attacks on SHA1 have to do with collision resistance. This means that any system relying on collision resistance should no longer be using SHA1. Digital signature schemes typically use a hash function to get a fixed-length value to sign, and that relies very much on collision resistance for security (as the Ars article points out).
However, the challenge-response mechanism in the YubiKey uses HMAC-SHA1. HMAC does NOT rely on collision resistance (this has actually been formally proven), and is thus not affected by this problem at all. HMAC-SHA1 is still considered secure.
The slot based challenge-response credentials use HMAC-SHA1, and we have no plans on changing this. However, the OATH applet available on the YubiKey NEO as well as YubiKey 4 provides HMAC-SHA256 in addition to HMAC-SHA1 (the YubiKey 4 even supports HMAC-SHA512 as well), but this applet needs to be invoked in a different way compared to the standard slots. For more information on that, go here:
https://developers.yubico.com/ykneo-oath/Protocol.html