RFC 1459 is famously sparse. It does not tell you everything you need to know to write a server.
In this case, what's missing is the distinction between a MODE command that queries an existing mode, and a MODE command that sets a new mode. In the case of a mode query, a client will receive a numeric reply that indicates the existing mode; in the case of altering a mode, a client will not receive a direct numeric reply unless there was an error. However, if the mode was successfully altered, then a client will recieve a MODE from the server informing it of the change.
So for example, if the client's nick is foo and it sends:
MODE foo
then this is querying its current usermode - it will expect a RPL_UMODEIS reply like:
:irc.example.org 221 foo :+i
If the client then sends:
MODE foo :+w
then this is altering its usermode - it will either get a numeric error like ERR_USERSDONTMATCH or an acknowledgement of the mode change:
:foo!foo@bar.com MODE foo :+w
Note that this acknowledgement is technically not a direct reply to the MODE - it's the server informing the client of a relevant change in its state, which happens to have been triggered by a client command.
A similar situation exists with channel modes. If a client queries the current channel modes with:
MODE #channel
then it will expect a RPL_CHANNELMODEIS response containing the current "simple" channel modes, and perhaps a RPL_CREATIONTIMEresponse giving the channel creation time. If it queries for the current ban list with:
MODE #channel b
then should get zero or more RPL_BANLIST responses, followed by a RPL_ENDOFBANLIST.
If instead a client tries to change a channel mode:
MODE #channel :+k zounds
then the direct reply will either be an error reply or nothing; and if the channel mode was actually changed, it will see the MODE command echoed back. In the latter case the successful MODE command will also be sent to the other members of the channel - this helps to illustrate that it's not really a direct reply to the initial MODE command, but an indirect response to it.