RAW says absolutely nothing about whether a spell is perceptible or not if its casting requires somatic, verbal, or material components.
To be perceptible, the casting of a spell must involve a verbal, somatic, or material component.
This means that if the spellcasting is perceptible, then it involves a verbal, somatic, or material component. It does not mean that if the casting of a spell involves verbal, somatic, or material components then it is perceptible.
With this alone, if we have at least one component present we don't know anything about whether or not the casting is perceptible. What can be concluded, is that if we have no components present, then we absolutely know that the spell is imperceptible.
The form of a material component doesn’t matter for the purposes of perception, whether it’s an object specified in the spell’s description, a component pouch, or a spellcasting focus.
What this concludes, is that if a spell would be perceived when using one form of material component, then it would be perceived using any different form of material component; and if the spell would not be perceived when using one form of material component, it would still be unperceived if you used any other form.
If the need for a spell’s components has been removed by a special ability, such as the sorcerer’s Subtle Spell feature or the Innate Spellcasting trait possessed by many creatures, the casting of the spell is imperceptible.
This only supports our first conclusion, if there are no spell components used in casting the spell, then the spell is imperceptible. it doesn't say anything about whether or not the spell would have been perceptible if there was still a need for the spell's components.
Back to my conclusion, if the spellcasting has components, then there isn't any rule for whether the spell is perceptible or not. It is left up to the DM.
Regarding what the rules as intended are: I mentioned in one of the comments to BlueMoon93's answer that I believe the intended rules are that all spells are perceptible if their casting includes any of the three components, I take that back, with experience I believe that is how things should be played, but I do not believe those are the intended rules.
I believe that the rules intended to leave the decision, for whether a spell which requires components is perceptible or not, in the hands of the DM, and this is what RAW does, because the only rule on whether a spell is perceptible or not, is that if it doesn't have any components it is absolutely not perceptible. This is how a lot of 5e rules are, they are left open for the DM to decide. So the answer to the question of whether a spell cast with subtle spell and an arcane focus can be counterspelled, or not, is that the DM gets to decide!
WotC has made it very apparent that 5e is intended to have fewer rules and a more open interpretation of the rules. This supports the that the rules may intend for the DM to determine when a spellcasting is perceptible.
Even though the intent of the rules is probably to give the DM the decision for whether a spellcasting is perceptible or not, I believe this is a terrible way to play. This is my opinion formed from both experience, and from seeing the negative experiences of others.
If the DM has the choice of whether or not casting spells is perceptible, I've seen it play it out two ways:
The first way I see it play out is that the DM decides that the spellcasting from the 'clever' NPCs and enemies becomes imperceptible, and when it comes to players they need subtle spell for their spells to be imperceptible (this is frustrating to players because on the whim of the DM, counterspell isn't even an option, and in more situations it pits the DM against the players).
The other way that I see it play out is that casting subtly is treated as a skill check of some sort: deception, performance, sleight of hand, arcana even (though more rarely), and in every situation I've seen or heard of, it wasn't handled properly, and it was too easy to fool everything (everything that can counterspell at the very least, in the monster manual, mages rarely have high perception or insight, of course then DMs fudge this, but they usually still make it too easy for mages to deceive with skill checks). This slows down the game because whenever a spell is cast a contest or ability check must be made. The worst part about treating the perceptibility of casting in this way is that those who are playing the sorcerer always cry foul about their feature being downplayed because the DM ruled it, and without any written rules to rationalize their loss; in their mind a rule was just homebrewed which takes their strength and gives a little bit of it to others. I've found that even players who aren't playing sorcerer for that game, but that are fond of the sorcerer, feel hurt when they see the rules treated in this way.