There was a time, like maybe 2 years ago, where the nanocrafter did run offline. At least that is what I remember. Anyway, it has been like this for a long time.
The technique that Zeddrick mentioned works really well. The main thing to keep in mind with doing this though is that the queue will not be completed when you log in if it was stalled when you logged off. For example, if you have a character queue up only product, like Silumin and Steel, but there is no ore to make the 1st step in the queue, it will stall. When you log back in later and there is the proper pures in the container, it will not have used them. It will still be stalled looking for ore.
To get around this, I will usually just add a step that I know will run as the 1st step, before I log off. Making hydrogen works great. It just gives you enough time to log off with a running queue.