Nothing. That's a risk you take when using any proprietary software, however.
I'd say the real world risk of this is (fairly) low, however if you're legitimately worried about it, you can use EncFS over a network share or FUSE file system, to your own systems. In which case you'd be using entirely open source software.
If you're that worried about security though, you'd probably be better off using a container based encryption method, anyway, as it wouldn't leak timestamps, file sizes and other data which could be sensitive. EncFS has some known issues with metadata leaking, but it's a decent solution for most general use cases.
I'd say the real world risk of this is (fairly) low, however if you're legitimately worried about it, you can use EncFS over a network share or FUSE file system, to your own systems. In which case you'd be using entirely open source software.
If you're that worried about security though, you'd probably be better off using a container based encryption method, anyway, as it wouldn't leak timestamps, file sizes and other data which could be sensitive. EncFS has some known issues with metadata leaking, but it's a decent solution for most general use cases.