@GeorgeHahn - thanks for the stylesheet which improves things in a high DPI environment. However, when I switch to an external monitor (which is standard DPI) then I subsequently find everything too large!
It looks like MarkdownPad uses Awesomium 1.6, and the latest version, 1.7.4 has support for detecting and adjusting to the device's DPI setting - http://docs.awesomium.net/?tc=P_Awesomium_Windows_Controls_WebControl_AdjustToDpi - so, aside from adding hi-res toolbar icons, an upgrade to Awesomium may resolve this issue.