Obviously they filter passwords and other sensitive data, but I think they should rightly have access to whatever they judge necessary to do their job.
There will always be people who have the ability to access data they are not supposed to, but in the end it comes down to who you will trust with your data.
To me, the transparency and contributions of 37signals qualifies them to have that trust. With that, I trust them to make good decisions about who they hire and what they store in their log files.
Of course, encryption per se is overkill for that. Something like ROT13 would do the trick.
I can trust someone and still not be comfortable if he accidentally see that I uploaded "how to file a divorce.pdf" for example.
If in the process of debugging the "," issue, a set of files is uncovered (including "how to file a divorce", tough. Ideally, the usernames could be unscrambled separately, so at least there's no immediate connection to a single user.
I'd think the number of apps doing this is much smaller than those that don't, and even then only in cases where file names are replaced with hashes or GUIDs for directory reasons, not for the sake of information security.