Why would a Bitcoin miner take less than the full reward? In "Mastering Bitcoin", the author notes (source):


  The maximum number of coins mined is the upper limit of possible mining rewards for bitcoin. In practice, a miner may intentionally mine a block taking less than the full reward. Such blocks have already been mined and more may be mined in the future resulting in a lower total issuance of the currency.


I understand that a possible answer is "just because" but I'm wondering if there are other reasons behind such an action.
Likely you're correct, it's not useful in practice. People could, however, use value destruction as an costly signal. 

Voting example; I run a poll of mining pools; number of Satoshis less than the full block reward, up to 5, is the vote for which of 5 proposed algorithms to run in the future. Once a majority of blocks over some time period vote for option X, everyone agrees to switch protocols. (This could allow identityless voting by miners.)

Commitment example; A miner can "promise" something, and commit the value destroyed as a signal that they are willing to do it. If a miner wants to extort the network, such commitment could be effective in showing that they are serious.