I suggest using the YAML built-in library provided by Bukkit to store passwords and associate them with a user. Then you can use a simple FileConfiguration#getString(String) to get the password associated with the user.
I don't know the exact implementation of SnakeYAML, but I assume it stores a line number table to reference the Node stored at the position to get the object, instead of a BufferedReader to read every line. This means a performance gain for large files.
And, two things: Unless you have hardware security issues, why encrypt passwords? And, I don't IO during runtime, hold reference to initial value at plugin startup in a collection, it's faster than disk read from file.