I believe the intention is for magic ammunition to be found in sets of one.
In other words, you're right about the implication. The 3e-ism of finding them in batches of 20 or 50 is long gone, and you need to recalibrate yourself and your players accordingly.
And no, I don't see +1 arrows as "worthless 95% of the time". That's an horribly pessimistic view of a plus bonus. Plus bonuses have always been some of the most coveted rewards of the game, especially so in 5E where they are so (comparatively) scarce.
If I would roll for magic ammo, I would probably roll 1d6 as the number of arrows the monster has left after the combat. (Yes, this means that if the adventurers are smart about taking out a monster before it can start using its bow, I'd give them the full six arrows)
Mathematically, their worth is dependent upon damage die modification and Natural Roll needed.
It's worth explicating this for those who want an idea of the overall improvement...
The raw improvement in average damage by raw TN needed, assuming no resistance. Resistance adds considerably more. If there's resistance, a high level fighter might need only a 2+ to hit a low-CR but resistant target, and then that +1 weapon is a huge improvement in average damage.
A typical case: Tier 1 fighter, +5 to hit, +3 damage, 1d8 weapon, average damage thus 7.5
Target 1: AC 13, non resistant.
Needs natural 8+, for a 65% chance of hit (CoH), and an average Damage per Hit (DPH) of 7.5, for an average damage per attack (DPA) of 4.875.
+1 weapon is 7+, 70% CoH, DPH=8.5, DPA=5.95; improvement is 22%.
Target 2: AC 13, resistant to slash
Needs 8+, 65% CoH, but DPH is much lower... DPH= 3.5 =(2,2,3,3,4,4,5,5)/8. DPA thus 2.275 (= 0.65 * 3.5)
The +1 weapon is still 70% CoH, DPH = 8.5, DPA = 5.95, improvement 161% (=(5.95/2.275)-1)
Target 3: Another fighter... AC 20. (Chain, shield, defensive style)
Needs nat 15+ to hit, CoH=0.25, DPH=7.5, DPA = 1.875
+1 needs 14+, CoH 0.3, DPH=8.5, DPA= 2.55, improvement = 36%
Target 4: same fighter, but the enemy warlock's made him resistant...
Non-magic CoH=25%, DPH again 3.5, DPA=0.875 (that's quite a drop)
+1 still 14+, CoH=30%, DPH=8.5, DPA=2.55, a 191% improvement in average damage per attack.
Ain't pretty, but it shows the principles, and just how freaking valuable that +1 sword is. 20% to 40% range vs normal targets, and 150% to 250% vs resistant ones.
(Note also: A +0 sword is a 0% improvement if the target isn't resistant, but it's +100% vs resistant targets)...