The conclusion in the link sums it up:
In conclusion, while EncFS is a useful tool, it ignores many standard
best-practices in cryptography. This is most likely due to it's old
age (originally developed before 2005), however, it is still being
used today, and needs to be updated.
The EncFS author says that a 2.0 version is being developed 1. This
would be a good time to fix the old problems.
EncFS is probably safe as long as the adversary only gets one copy of
the ciphertext and nothing more. EncFS is not safe if the adversary
has the opportunity to see two or more snapshots of the ciphertext at
different times. EncFS attempts to protect files from malicious
modification, but there are serious problems with this feature.
So the question you need to answer: How likely is it that an attacker can get hold of the ciphertext?
But that audit is from 2014 and was done on v1.7. v1.8 already fixes some of the issues mentioned in the audit:
The first EncFS 1.8 release candidate fixes two of the potential vulnerabilities mentioned in the security audit and brings a few other improvements:
- improve automatic test converage: also test reverse mode (make test)
- add per-file IVs based on the inode number to reverse mode to improve security
- add automatic benchmark (make benchmark)
- compare MAC in constant time
- add --nocache option
v1.8 came out in 2014 too.
From the project page:
Over the last 10 years, a number of good alternatives have grown up. Computing power has increased to the point where it is reasonable to encrypt the entire filesystem of personal computers (and even mobile phones!). On Linux, ecryptfs provides a nice dynamically mountable encrypted home directory, and is well integrated in distributions I use, such as Ubuntu.
EncFS has been dormant for a while. I've started cleaning up in order to try and provide a better base for a version 2, but whether EncFS flowers again depends upon community interest. In order to make it easier for anyone to contribute, it is moving a new home on Github. So if you're interested in EncFS, please dive in!
That is from 2013... I would consider the project dead if that was the latest news.
But it does list ecryptfs as an alternative for Ubuntu so have a look at that.