From the Help file for /font

The -d switch makes the font the default for that type of window, eg. for all channels, or all chats.

This does not work if there is no opened window of the type we are trying to apply the -d switch font to.

My suggestion would be that the font setting is applied even if there are no windows of that type opened. For example, you apply it to the query windows and there are no queries opened.