Correct, but I'm guessing the applications probably open files at a higher abstraction than a file handle [the curse/gift of Java], so it wouldn't be hard to decouple the file handle, and allow a trigger to close the file handle and sync on logout.
From a purely kernel perspective: it has been some time since I last looked at the kernel fs/dentry code, but from what I remember, the open file handle would hold refs for dentries that comprise the path [all the way up to mount root]. But even that wouldn't prevent other dentries from being cleared anyhow: only the open file would have unencrypted pages in the page cache. I would highly recommend reading the linux fscrypt code if you would like more details: it's very well structured and quite easy to get into!
Of course, the foolproof way would be to check lsof and nuke all processes that still have file handles open before logging out, but that's probably too much heresy :)