Using the /font command you can get round that limitation.
/font -ad -36 arial
That would set the active window to Arial at 36 points and make it the default for that window type. The '-' sign is important since otherwise the size is taken to mean pixels.

Unfortunately you can't set all mIRC windows to default to that font/fontsize at once, so you'll have to use that command in each window type at least once (ie. once in a Query Window, once in a Channel Window, etc.).