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 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.
