I've responded to questions like this one on more occasions than I'd like to type. BUT, Spring is coming and it wouldn't be fair to dodge this question. So, here goes ...
I don't know if cedar shakes have any r-value. If they do, I'd bet that it's negated by the fact that the shakes seal up the home less than having Homosote installed and the seams taped. My hunch in this case is NO.
As far as putting up vinyl over shakes, look at it from a couple of angles, literally. Do you think if you look down the 'line' of a home, that has vinyl over shakes, isn't going to show an inordinate amount of 'waving' due to the shakes, and the OSB or Homosote not being on a flat surface on which you put your vinyl? In short, I'd do the demolition and remove the shakes and put an exterior OSB or Homosote on for a smooth surface. Also, you can void a warranty if the subsurface doesn't meet the warranty requirements. So, before you knock off a shake or hang a vinyl sheet, check the warranty of the manufacturer you choose! Yet another angle ... Some day, you may want to sell the home. You'll more than likely have to disclose what's under there. Over a number of years, the siding is going to 'shift' on you if it's left on, and if it's noticible to the eye, whether it's waving or sagging, you'll have to tell if you're asked. Nay-nay. Demolition the shakes yourself. Put up Homosote or something, and work with a smoothe, straight, warrantyable, and sellable surface. AND, you won't have the 1.5" window problem you're inquiring about. Oh, doing the demo yourself can save you $75 - $150 per square (10' x 10' section).
New siding is installed, usually, anywhere from $3.00 to $4.50 per square foot (that's $300 - $450 per square). The more prep work you do, the less the price. If you put up the Homosote yourself, and tape the joints, you can save even more $$$.
Now, what would I do. I'd demo the shakes. Put up the Homosote, OSB, whatever. While the walls are 'down' you can add new electrical, new plumbing, etc., etc.. I ran 2-1" conduits from the basement to the attic at this time. I now have an easy way to get 110v and low voltage to the attic for use on the 2nd floor. (YOu can't mix the wiring in the same conduit!) I put in outside faucets on 2 more sides of the house. I now have outdoor electrical on all 4 sides of the home. New motion/spot lights too. I even put in an outdoor plug for Christmas lights so I can turn them on and off from the inside! ALL done BEFORE hanging up vinyl. Before you install new 'stuff', you need to check how far from the sheething you need to have the items mounted. In my case, it was 5/8" out from the sheething. THEN, I scraped and primed all the wood trim that would be left on the home after vinyling. It was capped with aluminum and now it won't rot. I put in soffits under the eaves, which was something I never had. Now the attic gets better air circulation in summer and winter. I then hired 2 friends to do the actual siding. It was a side job for them; they weren't a company. One guy was a window and door guy. The 2nd guy use to be a general contractor. (Just ask around. Someone in your neighborhood knows someone who does vinyl side work.) They knew what they were doing. I even bought the material. (They made a list for me.) I was the 3rd man on the job. For a job that was 22 squares, I saved over $5,000.00 by doing what I stated over the closest estimate. I got the dumpster too when the job was over. In the interim, I stacked everything in the driveway. It took a 15 yarder for everything.
Lastly, go to Ashland-Davis and read the Installation guide. You need to download Adobe Acrobat if you don't have it. At worst, go to Home Depot and ask for a manual. I do suggest you read it. This is the kind of job that requires a bit of research even if you're handy. If you don't start the job right, it's downhill from there.
I can go on and on and on. If you have any questions, post 'em up. I'll be listening. Or, ctc me via e-mail directly. For now, good luck!