I don't know anything about wired, but very few people need to be explicit feds for something like wired. Maybe one person high enough just has friends in the intelligence community, and that could more or less be enough - few or none are hired if their perspectives on key issues don't align with management.
It's a conspiracy theory, especially when talking about any specific media organization, but the intelligence agencies certainly did this before, and it came out in the Church committee. There are a few journalists who continue to work at big-name outlets despite being named as assets in the diplomatic cable leaks, for example. So it's not unreasonable to suggest, I'd say.