There is no difference! It's just a question of presentation when printing it.
That's exactly what it is; You print it as HEX. It is stored as a binary pattern. When you read from EEPROM you will always get that binary pattern. The difference is only how you present it.
Example: ASCII 'A', decimal 65 or hex 0x41 - this all is stored as binary pattern 0b0100 0001. You cannot see the difference when you read that pattern. You must know how you want to use it, as ASCII, decimal or hex ( or just as that pattern if every bit has its own meaning ).