Well, I've read the same things you have read about the capacitor dying a slow death on the shelf if it's not used. Since I was ignorant enough to buy my Whelen strobes when I started on the wings in 2003, I was worried that they may not work now. Fortunately, they fired right on up this spring when we tried them out in my shop (I'm a little further along in the build now).
I know that I may have just gotten lucky, but mine still worked after six years on the shelf. If I were going to do it over again, I'd wait to buy the strobes. You're going to need to ship a lot of other stuff down the road, and it won't cost that much more for Van's or Aircraft Spruce (or whoever) to ship the Whelen package along with other items you'll invariably need. That's my 2 cents.