I know one thing. Well, maybe one thing. For most objects to be fabricated, it is definitely a lot easier to not Boolean in the female threading in the holes, or not build the actual threaded hole surface. Because when you go to fabricate it, and you already booleaned in the threading to look good in a render, or snapshots, or whatever you gotta have a backup with just the holes.
Bascially when you go to convert it to fabricating instructions, whats gonna matter is the hole size, drill point angle at the end, what size tap to use machining it, how deep to thread it, etc… (not that you don’t know that)
If you do have the correct hole size, but unthreaded and you have your threaded bolts on a different layer, block, etc…
They will overlap each other, which I would imagine can make some functions of rhino behave differently. Be that what you are using with block instances, views etc or not. (not that you don’t know this, and I’m not even sure what command are affected by overlapping surfaces except joins and Boolean operations)
I made a determination that I would make the correct size holes in the model, have point groups for specific fittings, so that I know which holes are with which fittings, etc… Then have notes on the actual fabrication regarding the drilling, tapping, lengths, machine settings etc, elsewhere. Making the points with jigs, which could be your actual jig used for marking the stock. Or even designing your machining jigs around your design in rhino.
But, yes, the fancy renderings with the bolts in place, holes threaded would indeed look more professional for presentation. You will just need more versions of your model. Some for rendering, some just for fabrication. But if bolts are really the only thing that affects how you do 2d layouts, in the case that you can manage without actual renderings of the threads, it can save making a few less unneeded versions of the model. Unless of course you do need them, you are not the one fabricating, or instructing fabrication, and you do need to experiment in 3d to find proper thread lengths, and develop fantastic machining and assembly instructions.
As the saying goes though, there’s more than one way to skin a cat. And without saying, your cat pelts probably look a little prettier than mine.