Re: Apothecary gives duplicate recipes after syncing with golden nug.

I'm not saying it's serious and that they need to rush to fix it, I'm just pointing out a glitch caused by syncing. Since the golden nug is new there were bound to be issues. Maybe at some point they can make it so the game will recognize what recipes you already have and prevent duplication while still giving you the experience from completing quests. Maybe also remove things you already own from shops.

Schematics (and probably recipes... are there recipes you can buy from shops in the vanilla game?) you already own should already be removed from shops. Don't think I've ever seen a duplicate schematic. 
The duplicate recipe bug isn't really a glitch. Mods which made recipes available from shops also caused duplicates show up when you found the same recipes in chests etc. 
If you're really worried about the duplicates, you can always hold off on using the nug until later in the game. Or at least until you've completed the lyrium potion quest. 😛 

The antivan fire grenade recipe is still available at the shop/wagon at the Crossroads in the Hinterlands. I suspect the recipes for the resistance tonics will still be available in Val Royeaux. I haven't made it to the point where I can buy weapon and armor schematics to see if they were still there. The thing is, I have no idea when the threat of getting duplicates will pass. I'm pretty sure I will get a duplicate corrupting rune schematic when I talk to Dagna after recruiting her but I forget what happens after that.

There are serious glitches which are isolated incidents but the duplicate recipes are something that absolutely everyone who uses the golden nug will have to deal with. I do agree with your idea that we should be given the option to destroy duplicate recipes and schematics. That would be much easier than Bioware trying to prevent them from happening in the first place.

Honestly I might just avoid using the golden nug all together since it takes all of the excitement out of discovering new schematics from looting. Where's the fun in having the best things at the very beginning and steamrolling through the entire game? I might wait until the last opportunity to sync just so I can add what I get from future playthroughs to my collection.

They should still patch in a fix or work around for the duplicate recipes for the people who do use it though.

You shouldn't get ANY duplicate schematics- they work differently to recipes, and after several playthroughs with the nug, I have yet to encounter a duplicated schematic. This time I even waited until Skyhold before using the nug, just to check (well, that and I was doing as little as possible, going for the 'get to skyhold at level 5' trial achievement thing. Got it, yay). I think recipes duplicate because they're treated like requisitions (which you can get over and over again). Changing that would probably be a giant pain, and since patch 10 was supposed to (but hopefully won't be since Trespasser broke so many things) be the last patch ever, I doubt they intend to do anything about it. 😉 
As for having all the best stuff early on... When you've played the game 10 times or so, you might care less about such things. 😛 For me, it's doing different story stuff, etc. Plus, now I have shiny weird stuff from Trespasser to play with, like musical staffs!