The comlink in question, in hidden mode, will always be able to connect to the Matrix so long as it remains capable of wireless transmission/reception. This is because the comlink knows that the Matrix is out there to connect to and, following input from its OS and programs, will send out queries/commands/data requests as its user desires. It will then listen for the responses and accept them. By the simple virtue that it is activity that the comlink itself sent out, the response is considered authorized input. In short, the comlink in question tells the data where to go and then sits there waiting for it.
Now, that same comlink in question has, by virtue of going into hidden mode, turned off that background part of itself, that invisible-to-the-user foundation process that allows other devices to automatically 'know' that it is there. The other devices around will still send out their signals in all directions, but the comlink in question will ALWAYS refuse these background routing processes unless the process in question comes from: 1) a device that is on its white list (the list of comlinks/devices/accounts that are allowed to know that it exists even when hidden), or 2) data that is the result of its own actions/queries as described above.
To sum up, the two lines you've quoted from the books are not contradictory. They describe different aspects of normal comlink function. Going into hidden mode does not sever the comlink from the Matrix. It only makes it so it cannot be automatically detected by it. This is why nodes in active or passive mode are automatically picked up with a simple scan for nodes action, but hidden nodes require their own action which takes longer and is more action intensive, but still very possible. They are the Matrix equivalent of the shut-in who pretends they're not at home when the doorbell rings. Someone who's just passing by will accept that no one is there because no one answered the door. But it is very possible to determine that someone is actually there through other means (looking through windows, listening at the door, etc.).
EDIT: Spelling/grammar errors.