Skip up a few inches, and re-read the paragraph above the table (emphasis mine):
If your campaign allows for trade in magic items, rarity can also help you set prices for them. As the DM, you determine the value of an individual magic item based on its rarity. Suggested values are provided in the Magic Item Rarity table. The value of a consumable item, such as a potion or scroll, is typically half the value of a permanent item of the same rarity.
So, let's unpack that:
Campaigns that allow purchasing of magic items are the exception. From the paragraph below the table:
Unless you decide your campaign works otherwise, most magic items are so rare that they aren't available for purchase. […]
Even so, it's likely to remain similar to the market for fine art in the real world, with invitation-only auctions and a tendency to attract thieves.
So costing items is normally not even a thing that you are expected to do. If you do allow purchasing of Very Rare items (and allow Very Rare items to be bought in 20× bundles!), you're leaving the trail and embarking into wilderness with only a few landmarks to help you. Judgement and discretion is expected and required when choosing that course.
The values provides are suggested values, to help give a ballpark value. These are really large ranges, and ignoring the suggestion when it makes sense to do otherwise is expected and necessary. Again, judgement and discretion is required. (This is a general truth when engaging with the magic item section of the game. It's in your hands to make magic items add awesome to your campaign or ruin it.)
Arrows are consumables, to you have to divide the suggested values in half before even considering them to be a meaningful suggestion. Recalculating the example of a quiver of 20 arrows +3 at 5,001gp a pop: it should be 2,500gp each, for a minimum suggested value of 50,000gp for twenty.
Additionally, yes, rarity (and therefore suggested price) is per arrow +3 rather than per bundle, as seen from the singleton nature of the Ammunition description on page 150.
Given the flatness of the power curve in D&D 5e, that's not an unreasonable amount for a quiver full of +3 to hit. But again, that's assuming that you have designed a magic item economy for your world, and assuming that's the price you want to set for a quiver full of these. (For a matched set of 20 Very Rare items, you may actually want to increase the cost! Like in life, things like this are more valuable in sets than singletons.)
In conclusion, this is a very loose framework that you're expected to take up, inspect, toy with, and mangle to your satisfaction. In order to maximally leverage our smarts as human beings, and to avoid creating a rigid system that is impossible to debug for exploits, the system was designed to be processed by an intelligent, judicious human mind rather than cranked through a calculation machine.
The result is something that is flexible and powerful, and mediated by an intelligent agent (you, the DM) to prevent untoward bugs and exploits.
You've already noticed something that isn't to your satisfaction — good! That is the first step to making it work for you. Based on your dislike of the suggestion, adjust it to where you want it. Remind yourself that this game doesn't have a balanced gold or magic item economy and is designed from the ground up to not assume or need one. You have as much room to tweak and adjust as your conscience says you need.
This is all assuming that you're the DM, of course. If you're a player, the DMG is almost entirely useless to you, because none of the material is designed to be useful except as inputs to an actual DM's choices, which are then relayed to the players for a specific campaign.
