To sum up the mechanics of counterspell:
If a creature with counterspell available can perceive any spell within range being cast, they can attempt to counter it. They don't need to know what spell it is, or even have it on their class list to make the counter. Based on this, and what I gather from your context, the short answer is: yes the NPC could have cast counterspell.
Let's tackle the issues one at a time with this knowledge:
Issue 1:
The NPC doesn't have to know that a silence spell is being cast. All they need to know is that a spell is being cast at all. Counterspell counters any spell after all. How would they know that a spell is being cast? Because silence has verbal and somatic components. So, as long as the NPC can see or hear the caster casting something, the NPC has the option to counterspell it.
Issue 2:
Yes. It's been established in the Sage Advice Compendium that (emphasis mine):
If a spell that’s altered by Subtle Spell has no material component, then it’s impossible for anyone to perceive the spell being cast. So, since you can’t see the casting, counterspell is of no use.
So, if the NPC can't perceive the spell being cast, then they can't counterspell it. In most circumstances (casting during combat or from a different room) it's up to the DM to determine if the NPC can perceive the casting. But if the DM rules (or is convinced) that the NPC can't perceive the casting, then the NPC can't counterspell. In this case, I assume that the NPC could see you casting, and you were within range, so counterspell would have been a legal reaction.
Issue 3:
It could, though it doesn't have to. There are some optional rules that allow creatures to identify a spell as it's being cast, but those are... well... optional. Unfortunately, the DM just has to make a call on what this particular NPC would do, and stick to it. There is no rule pulling the decision one way or another. It's reasonable for the DM to rule that the NPC would take the risk and not counterspell whatever you decide to cast. But, it's just as reasonable for them to rule that the NPC would assume that any spell you cast is a threat that can't be allowed to pass, and so would counterspell it regardless of what it turned out to be.
Issue 4:
Technically, a creature doesn't automatically know anything about the effect of whatever spell a different creature is in the process of casting. But the rules are, again, silent on this matter beyond that. So, if the group decided that minimizing metagaming is something that they want to strive for, neither they, nor the DM should know what spell is cast before deciding to counterspell. But that is a conversation that you all will need to have as a group. Some groups are more lenient where everyone knows what spells are being flung around. And still others let the players know what the enemies cast, but not the other way around. You all have to decide for yourselves what would be the most fun.
Your only option is to be careful
The shape of spell areas is fixed and nothing in the book gives you permission to directly change it. There are some features that deal with this problem (like sculpt spells for evocation wizards), but none apply to silence. As to casting in relation to a wall:
To target something, you must have a clear path to it, so it can't be
behind total cover. If you place an area of effect at a point that you
can't see and an obstruction, such as a wall, is between you and that
point, the point of origin comes into being on the near side of that
obstruction. (PHB 204)
So you do not necessarily have to be able to see the center (it could be dark or obscured), but if there is a wall, it will not work as you intended. There is one thing that you could make use of, though:
A spell's effect expands in straight lines from the point of origin.
If no unblocked straight line extends from the point of origin to a
location within the area of effect, that location isn't included in
the spell's area. To block one of these imaginary lines, an
obstruction must provide total cover (PHB 204)
So if you position the center right, the wall could block the area the guard is in from the effect.
Best Answer
Silence does nothing to a readied disintegrate
The disintegrate has already been fully cast and its power held. All the components have already been performed including any verbal components which silence could have disrupted (had the effect been present during the actual casting). Thus, silence cannot affect the completely readied disintegrate. RIP Marco.
This applies to spells in general as well. The only edge cases (as pointed out by @Slagmoth) are some spells that require a target that can hear you or depend on some sort of audible effect (eg. suggestion). For these spells, silence would prevent their effects. However, for any other spell, silence will do nothing once the spell has already been cast and readied.