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I am using PBKDF2 encryption to hash password with salt.
should I store hashed password and salt in database after applying base64 encoding?
If I do use the encoding, then the password length becomes 88 from 64, which requires more storage than when I am not using it.
What are advantages and disadvantages for using the encoding?
should I apply it to salts too?
From the security side, there is no difference between storing pure bytes, and storing a Base64-encoding of them.
If you store pure bytes, make sure you select the right datatype (e.g. a binary one, not a character one) for your column. If you store base64, you can use a character column with US-ASCII encoding.
Base64 has the advantage that a human can more easily look at the data and see if it is the same as some other, but this is about it – you could easily do the encoding after querying the data, too.