For orders of 100+ units, we can flip the headers around (and you also get a 20% discount off MSRP at this volume). We have had a handful of requests for headerless boards over the year, albeit in small quantities for prototyping.
Just let us know what you need and I'll see what we can do
![:)](http://forums.netduino.com/public/style_emoticons/default/smile.png)
And yes, as you surmised: those larger holes on Netduino are mounting holes.
Chris