If this encryption is still the same as it used to be a couple of years ago (encfs, IIRC), it's good they aren't. I stumbled on that multiple times before I learned not to turn this shit on. Every time on a new installation (which doesn't happen that often, so it's natural I was forgetting) I chose "do encrypt" option (because why not?), it was working perfectly fine long enough for me to settle in, and then one day I would be downloading some books via torrents, and torrent wouldn't proceed because of "filepath too long" (which was very confusing, because how could that be on Ext4, given it's perfectly fine for other peers, who must be on NTFS, most likely), and I had to spend time disabling encfs (I guess it wasn't that easy either: creating a new user was the quickest option) in order for things to start working.

So, finally I learned just not to use file-based encryption, except for minor stuff like dropbox directory.