in 1/72nd scale I think you can safely lose most of the rivets, or at least rub them down until you can only just see them on the bare plastic. Go & look at the Shack from around 50 feet away, where did those rivets go to? all you'll see is paint & shadows. This subject has been discussed before on the forum, mostly it came down to personal taste & how you want your model to look.
If you want to put rivets on the replacement parts, find a good jeweller & ask about a ponce wheel. Imagine a cog from your watch on a stick, the cog can rotate as you wheel it across a surface. As it does so it makes 'dimples'. That's a ponce wheel.
I've never used one but I've seen the results from one & it looks good.
Remember that the Shack kit is very old and the surface is overdetailed as were most kits of that era. Having said that, a common RAF name for the Shack was;
3 million rivets flying in formation!