crypt hasn’t been audited externally. However it has received quite a bit of scrutiny from participants in the project.
I’ve written up how it works here: http://rclone.org/crypt/#file-formats
The file encryption is based on NACL secretbox which was designed by DJB one of the world’s best known cryptographers and has very strong confidentiality and integrity. The weakest part is the file name encryption which is difficult to do and still preserve properties that rclone relies on.
There is a project to implement a higher security file name encryption mode here: https://github.com/ncw/rclone/issues/637 which will tradeoff some speed and resilience for better encryption of the file names. The file data encryption won’t change though.