The A nuts are only $7.95 for eight thru eTrailer online.
With regards to having to remove the end caps, that really isn't a big deal. I placed 12 A nuts in each Yakima rail. I buy whatever size stainless bolt, and lock washer I need at the local Ace Hardware. I then mounted my solar panels, canoe racks, some tie downs and my fly rod holder. I will say that since I didn't mount everything at the same type I did need to unmount things at times to position the nuts where I needed them.
I still have a couple of unused A nuts in the tracks, just in case I think of something else to mount.