For air penetration, rather than a shiplap you may consider using a tongue and groove on the planking, with the tongue facing up so water doesn't collect in the groove. This just gives you 1 more bend for the air to get around. Also, a tongue and groove is easily sealed with tar or some such (I would not recommend silicone). See if you can find some pine tar for this (it will be hidden away inside the groove) or if you can't asphalt will work.

2 or 3" plank siding and/or infill is very common in Switzerland, whose building style I have been studying, so I have learned quite a bit about how to execute it.

One traditional Swiss wall system is probably very similar to what you are thinking, a wall infilled with 'lehmbau' which is often a straw/clay setup, or may just be clay. The exterior is covered with thick planking nailed onto the timbers, and the inside is usually covered with wood paneling, but in a more utilitarian setting may be covered with reed and plaster. The timbers are thus totally concealed. Alternately, the infill may be random stone mortared with clay or lime.