[java] Java, How to implement a Shift Cipher (Caesar Cipher)

The warning is due to you attempting to add an integer (int shift = 3) to a character value. You can change the data type to char if you want to avoid that.

A char is 16 bits, an int is 32.

char shift = 3;
// ...
eMessage[i] = (message[i] + shift) % (char)letters.length;

As an aside, you can simplify the following:

char[] message = {'o', 'n', 'c', 'e', 'u', 'p', 'o', 'n', 'a', 't', 'i', 'm', 'e'}; 

To:

char[] message = "onceuponatime".toCharArray();