This attack targets the nuts and bolts of how the Windows platform actually implements TLS; a vulnerability in CryptoAPI that allowed you spoof any ECC certificate would presumably break all of TLS. What might mitigate this in Windows Software Update would be some kind of key pinning that prevented arbitrary certificates from being used.

Later

Dmitri Alperovitch at Crowdstrike says this doesn't impact Windows Update.

It does allow you to modify TLS streams (the WU downloads), and code signing (checking that a binary can run), but it is unclear if any of the trusted WU validation keys (confirming the update is from a signed manifest) are ECC.

So: maybe.

Only if Microsoft is using ECC for its Windows Update certificates. I would guess not given how many past OS versions Windows Update has to support.