Shakes don't present too much of a problem as they are usually used on the roof. On occasions when they are used on walls, you're right...they are thicker, stiffer, and generally have more texture (hand or machine split instead of sawn) than shingles.
Shingles, however, can contact the housewrap for the upper 6 inches or so of the shingle. obviously, it depends on the size of the shingle and the exposure. However, the upper portions of shingles are pretty flexible and easily conform to lay flat on the housewrap.
Shingles and shakes can perform "okay" if set directly against the wrapped sheathing. If they are set on furring strips or cedar breather, you 'll greatly improve not just the life of the shingle, but how well and how long it will hold a film finish.
No arguments from me that moisture can escape from behind shingles quite easily. However, water does get behind shingles, and once it dissolves the surfactants and brings them on the spun-poly housewrap...the process has begun.
The process is less likley, and less prevalent with shingles then it is with claps, mostly because, as you mentioned, shingles allow moisture to pass over/under/around them much more readily than do claps.
I'm in coastal New England. Here, cedar shingles are ALWAYS furred out, ALWAYS. Shakes are always furred out on roofs, too. Either with furring strips, or since its introduction, with a product like cedar breather. On walls, some use a spun-poly wrap, many still use tar paper. As to a house being able to breath with tar paper, it's not tough with un-taped seams and all those nail holes.
Still, I've never seen a failure with shakes or shingles...but then I've never seen an installation where they were applied DIRECTLY on a spun-poly housewrap. They've always been furred out. Regional differences? Who knows?
Not everyone backprimes around here, but it is getting much more common, especially since factory primed claps became more the norm than the exception. Before factory priming, the painter would have to prime the boards, then the siders would come back and hang the siding, then the painters would come back again to paint/stain. A logistical no-no. If it ain't easy and cost-effective, it ain't gonna happen.
After having too many callbacks for blotchy siding, many painters and GC's in my area require that the cedar claps be backprimed prior to installation.
Houses today are built better than in years past. Better foundation-to-ridgeline vapor diffusion barriers, better exhaust for in-house sources of moisture (stove/bath/shower/laundry vents), dehumidification via central air...all these things contribute to controlling in-house moisture.
Spun-poly housewraps can be a good thing...but don't be surprised to see a backlash against it and a renewed demand for good old tar paper in upcoming years.
Surprisingly, you'll see tar paper more on high-end construction than on tract-type housing. Uneducated consumers consider spun-poly housewraps to be a symbol of quality in construction, and many buiders are more than happy to put the extra $$$ into the house to show that they know how to build right...especially since most tract-type housing is sided with either vinyl, or maybe a cementitious product like Hardie claps...thus taking cedar out of the equation. I think you;ll see products like Tyvek behind vinyl and Hardie for years to come. It works well there.
You'll probably hear more about this in the future. Building Science is a growing field. Too bad pics can't be uploaded...I've got some great pics of housewrap failure laying around here somewhere...
If I hear anything new, or discover another source of info, I'll try to pass it along.
Henry...Yup...nickname came from "Mongo" in Blazing Saddles. It's a long story...and, again, I've gone on too long already.