The mechanical and automatic nature of evidence gathering is a real difference, and goes well to argue against NSA-style warrantless crawling.
I think for warrants, though, we're looking at a different beast. By their nature they are targeted. And people have been compelled to provide passwords in the court of law(See [0]). The right against self-incrimination is relatively narrow, so as to not hinder the government's discoverability powers too much.
I think the one thing about this, though, is that people can already be compelled through legal means to unlock things. There is a reading of the Apple case that they are being compelled to unlock something for which they have the key.
Generally, it feels like outlawing encryption isn't necessary for the gov't to pursue the discovery phase of an arrest. There are already a good amount of legal means to compel people to unlock the doors.
[0]:https://en.wikipedia.org/wiki/Key_disclosure_law#United_Stat...