From the point of view of security, there is no problem with a key being longer than the ciphertext – 3DES has a 168-bit keysize and a 64-bit blocksize so for small messages it results in a ciphertext shorter than the key (at least without counting an IV).

However, in most [block cipher modes][1] the message gets padded up to a multiple of the blocksize, so a single 16-bit integer would result in at least 64 bits of ciphertext. That can get a bit inefficient if you have a lot of very small fields.


  [1]: https://crypto.stackexchange.com/questions/tagged/modes-of-operation