Q:

Is there a way to deposit caps?

I currently have 87,621 caps on me.  With the Nuka World DLC, the addition of the Scav! magazines give you some special abilities.  One of the magazines give you more strength and endurance based upon the number of caps you have. The bonuses are:

+1 Strength & +1 Endurance if you have <= 10,000 caps.
+2 Strength & +2 Endurance if you have <= 1,000 caps.
+3 Strength & +3 Endurance if you have <= 100 caps.

I would love to be able to take advantage of this magazine especially since I have some powerful melee weapons and 10 strength already. 
Can you deposit caps in a container or is that not possible?  

A:

I'm not absolutely certain this works in a vanilla game (I've got a ton of mods, so one of them may be causing this to work when it shouldn't), but in my game I'm able to buy and sell certain ammo at 1 or 2 caps each way. I have level 3 Cap Collector (although only 1 and 2 matter here), as well as 17 Charisma and 5 ranks of Junktown Vendor. .45, 5.56, and 10mm rounds go for 2 caps each, while flares, railway spikes, and flamer fuel go for 1 cap each. This means I can buy a bunch of ammo, throw it in a box somewhere, then later sell it all for the exact same price. But with almost 130k caps, it would probably take me quite a while. Percy, the Mr. Handy in Diamond City, has 601 caps worth in one trip. I could probably get about that from one of my settlement shops, and some extra from Goodneighbor and so forth, but that's still 40+ total resets. At least you can sell to six 600-800 cap vendors in your settlement each reset with the level 3 Cap Collector perk so the sellback is a bit shorter. 
If you're on PC, there is a mod that lets you create a pile of caps in your settlement, then scrap said pile for the caps' value, which has the same effect as throwing them in a container, although the biggest cap pile is 1000 caps so it will take a while when you're in the vicinity of 100k caps. (It also does other stuff you may or may not like, such as 1000 caps weighs 10 lbs.)
I don't know of an easy way in the vanilla game to store lots of caps one-to-one, but if you've got so many caps you just don't care anymore, you can always spend them all on gear. Then you re-sell the gear later to get some/most of your caps back. I buy Fusion cores at 240 and sell them at 160, so I'm losing 80 caps each, or 33%. I can't just buy 541 of them at once to use up all my caps, so it's a kind of slow process, but I can get about the same exchange rate for anything, so missile launchers and legendaries would be a good place to start if you don't feel like buying little piles of ammo at a time. Using this method, I was able to buy 16371 caps worth of stuff from Percy, then sell everything back for about 9548 caps (42% loss) after throwing all my charisma-boosting clothing in a box. Using the console to change my charisma and/or remove the Cap Collector perks, I got the following values:

        CC Rank
0
1
2
0
2
1
2
2
2
2
2

        Cha
1
1
1
10
5
10
8
9
10
11
19

        Buy
37192
32191
25950
23835
21412
19144
17984
16616
16371
16365
16371

        Sell
4639
4871
5719
6633
6948
7850
8150
8668
9546
9974
11055

        Loss
88%
85%
78%
72%
68%
59%
54%
48%
42%
39%
33%

Alternately, you can build a bunch of shops in your settlement at 100-500 caps each, then scrap them for half value later. If you run into the building cap, you can store the extra shops, then rebuild for free and scrap them later. However, you'll run into the slight problem that you can't build more of that type later or you just build the stored ones, so you need to switch shop type. There's also the problem that shops cost various resources, which you may or may not have tons of.
If you don't care about the extra resources (8 steel or 5 wood/3 steel per stall), you're better off using the shops to "store" your caps until you have Cap Collector rank 2 and charisma of 9+ (or higher charisma with lower ranks). From here, you can max out charisma at 32 (vanilla) or 43 (Far Harbor), but by 16 charisma you've capped the game's buy/sell values even without perks. It hits minimum at 120% buy and maximum at 80% sell, so you're getting back 80/120 = 2/3, which is the 33% loss I was seeing at 17+ charisma and all the perks. Remember that I have 5 ranks of the Junktown Vendor perk, so your numbers will be slightly higher or lower if you have different ranks there.
Even with low charisma, you can use a hat (+1), black-rim/fashionable glasses (+1), summer shorts (+2 and allows arm/leg armor slots), "sharp" legendary arm/leg armor pieces (+1 each for +4 total). This gets you to +8 without consumables. Then +5 from craftable grape Mentats and +1 for most easily-obtained alcohol gets you to 15 charisma with a base charisma of 1. Combined with the +10% price boost from the Mentats, that's going to get you close to or over the cap without any special points invested, and some harder-to-get chems should get you the rest of the way (and really, if you've got the legendaries, you can probably pick up the bobblehead to hit 16). The hardest part will be finding all the legendaries, but at least it doesn't matter how good it is (so a low-level raider arm is just as good as heavy synth armor here).
With the Far Harbor expansion, you can get the Dapper Gent hat (+2 instead of +1), and two pieces of "unyielding" armor (+3 each is +6 vs the +4 from four pieces of "sharp" armor, so it should be easier to attain). If you get an unyielding chest piece, you can swap the summer shorts for the green shirt an combat boots outfit (only +1, but you can't use a chest with summer shorts, so this with a +3 from the chest is 2 better than the shorts). With five pieces of unyielding and the dapper hat you get +11 over vanilla (+15 vs. +4 for affixes is +11, then +1 vs. +2 for clothes is canceled by the +2 vs. +1 for the hat), which means you don't need any consumables at 1 charisma. Unyielding does require you to be at less than 25% health, so it's best to play without health regen. Then jump off a cliff or something.

