The RPC method to change the passphrase is: walletpassphrasechange (it's right at the bottom of the RPC calls listed here:
https://en.bitcoin.it/wiki/Original_Bitcoin_client/API_calls_list).
As regarding whether that matters when running a server it just depends upon whether that server is going to *use* a wallet (it is actually possible now to start up the server without a wallet at all).
If your bitcoin server doesn't need a wallet then perhaps consider using the -disablewallet option.