Yes, the Wyvern is probably intended to have disadvantage.
While Word of God could always overturn this (but it didn't), it seems pretty clear that the intent is for this to apply to reach attacks. They have the key phrase "ranged attack" and use it elsewhere in the rules (e.g. in the Monk's deflect arrows ability). This heavily implies that the more awkward wording is there for a reason.
They might have worded it this way so that ranged attacks made from melee are normal, rather than disadvantaged. But I suspect this case is less likely than the reach attack one (your mileage may vary).
In other words, it's not a case where it looks like they used simple language and forgot about some corner cases, like the interaction between druids and lethal damage.
As to why this would be the case, consider that a large wyvern doesn't have a 10' body with a long head that sits 10' away. The entire wyvern occupies a 10'x10' space, and stretches or pounces when it needs to attack outside of reach. This kind of stretching / pouncing will inherently limit the creature's attack vectors, perhaps in a way that dropping to the ground will help.
In other words, the monster isn't right there. The monster is still 10' away.
Also remember that the monster doesn't have to stay at range. As soon as they drop prone, it can close to within 5' and start taking advantage on its attacks.
From a mechanical standpoint, this makes prone a general strategy to take for things attacking you that you can't reach and/or luring things into melee. This simplifies the mechanical design, and helps avoid loopholes.
As a house rule, you can certainly scale down the effectiveness of the prone condition. It's unlikely to break much with the current corpus of monsters. However, doing so will always compete with simply closing to melee and gaining advantage... And it is unlikely that this will be brought into the official rules (although maybe it will! Sloppy templating, etc.).
Sorry, but No
The Key Word here is Attack. Attacks as defined in the PHB are D20 rolls against AC.
From PHB, 194
If there’s ever any question whether something you’re doing counts as an attack, the rule is simple: if you’re making an attack roll, you’re making an attack.
Critical Hits are defined on page 194 (emphasis mine),
If the d20 roll for an attack is a 20, the attack hits regardless of any modifiers or the target’s AC. In addition, the attack is a critical hit, as explained later in this chapter.
Acid Splash is a Save-based Spell and doesn't qualify as an Attack for a Critical hit, since there is no d20 roll for attack.
Best Answer
The rules that you've quoted are pretty clear. You gain advantage when attacking unconscious creatures, and you gain disadvantage when attacking prone creatures from further than 5 feet away. If you have both advantage and disadvantage — you're attacking an unconscious creature from further than 5 feet away — you get neither, instead.