If you have more than one clockwork amulet could you use its function multiple times in one day? And if so is that balanced?

Yes. And yes? Getting multiples shouldn't be that easy even for a common magic item. If a DM wants to limit it, they can.

The main problem I'm having is that one of my players has a +12(enough to hit ancient dragons using the clockwork amulet) to hit at level 4 and the rest of them have at least a +6 and they're about to have a 2 year time skip where they all plan to spend the whole time making them. I'm afraid that they once they have a hundred of them they'll just never miss again and possibly more importantly never roll again. All of the crafting is done through official rules and they have resources and the recipe.

 Tell them that there is a special required material component that is rare, and they have to adventure for, and there are limited resources for.

How do they have a +12 to hit at level 4?

How the heck do they have a +12 to hit at 4th level?  At max they can have a +7 before magic items (or +9 if archery fighting style). 

As for having hundreds of them, realistically, there is no way they can wear that many amulets at the same time.  They would need a bag of holding to have that many and it takes an action to retrieve one object from a bag of holding.

And when it comes to crafting them, put a limit on the materials that are available for them to purchase.  Just because they have the gold does not mean shops have the proper materials to make a whole bunch.

Also, if they insist on using too many at a time, make a rule that using too much law magic at once will eventually make the universe have to balance out with Wild Magic. This could make it so whenever someone casts a spell within 30 feet of them each time after they use the amulet, they roll on the Wild Magic Surge table.

Quote from Yasesril >>

The main problem I'm having is that one of my players has a +12(enough to hit ancient dragons using the clockwork amulet) to hit at level 4 and the rest of them have at least a +6 and they're about to have a 2 year time skip where they all plan to spend the whole time making them. I'm afraid that they once they have a hundred of them they'll just never miss again and possibly more importantly never roll again. All of the crafting is done through official rules and they have resources and the recipe.

 It sounds like the first problem is the +5 (or higher) magic weapon you gave them to be able to hit ancient dragons with.

The second problem is that these things should cost 50gp worth of material, an optional special item if you choose, and 1 week of work per amulet. At level 4 it is reasonable to have enough materials to craft maybe around 8 of them. If they plan to craft 100, then you have given them around 4000 too much money.

Lastly, just because they don't have an official weight doesn't mean these things are weightless. Make them weigh 2lb each and see how many the PCs want hanging on their necks.

The official rules give you a handful of ways to deal with your problem.

My bad his to hit is a +11. It comes from having a 22 in dex because of blood hunter and a plus one hand crossbow and archery.

And when it comes to materials they are sitting in a city overflowing with materials especially common level materials. As for using them they dont need to have them all ob at once, if they are wearing like 10 a fight that should be enough to win then they just change them out after. 

I could add something to limit the use by causing wild magic like suggested.

I assume you're talking about the Celerity mutagen? If they want to use that all the time a very simple counter is just throwing Wisdom saves at them. I'm guessing they rolled well in stats to have a 19 Dex at level 4?

I would just talk with the player in question, you're okay with them crafting magical items, but don't abuse the game rules. One maybe two amulets you're cool with but anything more than that just say no or have a small army of modrons intervene.

If you decided to give them the 5000 gp, recipe, and not require special items (or otherwise provide those for them as well) to be able to craft 100 clockwork amulets, you can't be upset when they do.

Maybe make a rule that if they are wearing multiple, they use all of their charges at once, so they have to wear one at a time and swap between uses (which uses an action in combat). That should serve as a ladder for the hole you find yourself in.

You could also give your monsters higher AC. To preserve balance you could lower their saving throws, rewarding players that use abilities that don't require attack rolls. Maybe the AC is 23 but all attacks against them have advantage (you can't take advantage of advantage if you forgo your roll to use the amulet!) 

EDIT: You may only have to do this for a session or two before they get the point that you feel like the amulets are ruining the fun and maybe everything can go back to normal. If they are excited about trying it I wouldn't wanna just shoot it down straight up but you have the right (and duty?!) to re-balance things to keep it difficult. I wouldn't do this to every creature either or they will feel equally disappointed as a direct "no" but a challenging mini-boss that is tailored to thwart their scheme could spark a conversation about the balance.

My DM uses video game equipment slots so you can only wear one amulet at a time. And if you want to swap it out it takes an action to change them. So if they want to forgo their action swap then they are attacking every other turn. 

And why the 2 year time skip? Is it a campaign driven thing?

Or, as a DM, you can just say sorry you made a mistake to provide everything to have them break the game so they can only make one per player max. Or don’t allow them to make any. Or ramp up all your monsters AC’s etc to compensate.

Everyone makes mistakes. Hopefully you can talk to the players and walk some of this back. 

I am extremely late to this reply but a common rule worth noting [for others who view this topic in the future], is that effects cant stack.

I would make as a corally, that stockpiling a particular effect should lean into this rule but at the very least isn't in the spirit of the game.

That said I have made tons of mistakes in my DM'ing and when I have made a mistake just own it and apologise explaining that this kind of move [stockpiling these items] is actually make much more work for you as a DM behind the scenes in your prep.

Most reasonable players might gripe a bit but recognise that the game is meant to be fun for all of you not just the players.