It is your rifle do with it want you desire. The stock will not be affected by your brake and suppressor which can be readily removed (I assume) and a threaded cover placed on the barrel, like one of my 338 Win Mags can be configured (a Browning stainless and black synthetic stocked one which I use hunting elk).
I also have a beautifully stocked and engraved 338 Win Mag that I leave alone. The man sold me the rifle at considerably less than market value. Thinking back he wanted me to have it.
I did purchase a Browning stainless and black plastic stock rifle to hunt with in the mountains of Utah near in the eastern Unita mountains. That rifle has signs of hiking all over through the rocks, etc with my brother. That is my "collectors grade" 338 Win Mag, engraved, etc
It's just a barrel. A disposable, perishable, that is only useful to you anyway. There is never resale value in a used barrel, and whoever buys the gun from you would anticipate replacing it soon/immediately.
Make it what serves your the best. Thread it, brake it, hell, integrally suppress it. If it is a collector piece take the original barrel off rebarrel it and restock it and keep those in your safe so you can always put it back to original
Depends on the rifle. Something nice, and traditional or vintage, then, yes, it will lower the resale value. For the most part, people who will pony extra up for very nice wood, or a classic or vintage rifle in good shape, are into the aesthetics/traditionalism and don't want to see a a brake on the muzzle. For example, a Winchester M70 pre-64 in very good shape - for sure, putting on a brake/suppressor will lower its resale value. The same can be said for a nice old Sako or Weatherby.
Whether you are willing to take the hit is a different question and is solely your decision.
Of course, there are always exceptions. And, people are always happy to trash someone else's rifle.
There are a lot more shooters than collectors. If the rifle is truly collectible right now. Make it work for you. Only if it’s sentimental can I see a twinge of thinking about it. None of the above rides to the point of blasphemy.