Yes, you can use Cutting Words even against a spell with Subtle Spell used on it
Counterspell's trigger is:
when you see a creature within 60 feet of you casting a spell
If used, the sorcerer's Subtle Spell metamagic option effectively makes it impossible to perceive the casting of a spell with only somatic and verbal components - and thus impossible to counterspell.
Unlike counterspell, however, the College of Lore bard's Cutting Words feature doesn't require seeing a creature "casting a spell. The feature description states:
When a creature that you can see within 60 feet of you makes an attack roll, an ability check, or a damage roll, you can use your reaction to expend one of your uses of Bardic Inspiration, rolling a Bardic Inspiration die and subtracting the number rolled from the creature’s roll.
Cutting Words doesn't rely on you seeing someone "casting a spell". It doesn't even rely on you seeing someone "making an attack roll/ability check/damage roll", because those are simply mechanical abstractions of what's actually happening in-universe. The primary things it requires are that you see the creature and that it be within 60 feet of you.
As a result, you can basically attempt to use Cutting Words on the attack or damage roll or ability check of any creature you see within 60 feet.
Of course, your DM may houserule that you need to be able to visibly perceive that the creature is doing something in order to react to it, but that's just up to your DM (and the players).
This is answered, if not very directly, in the Sage Advice Compendium (version 2.3, if it matters).
Do you always know when you’re under the effect of a spell?
[...]
Some spells are so subtle that you might not know you were ever under their effects. A prime example of that sort of spell is suggestion. Assuming you failed to notice the spellcaster casting the spell, you might simply remember the caster saying, “The treasure you’re looking for isn’t here. Go look for it in the room at the top of the next tower.” You failed your saving throw, and off you went to the other tower, thinking it was your idea to go there.
Apparently, what the caster says is not part of "casting the spell".
Generally speaking, if a spell's text defines some activity that is required to use a spell, you still have to do that thing even if you can avoid using components of that type.
For example, if you have to touch the target of a spell, removing the somatic component doesn't remove the need to touch the target. By the same logic, removing the verbal component of suggestion doesn't remove the need to speak the suggestion; it just means you don't have to intone any words of power along the way, or present it in such a way that it is obviously spellcasting.
So judging by the Sage Advice example, you do have to speak, but you can speak conversationally, and there would be no clear indication that you're doing magic to either the target or the bystanders. (They still might guess that you'd used magic if you said something really absurd and the target immediately went along with it, though.)
There's still a material component, so you'd technically need to have the components in hand or be holding an arcane focus, but since there's no somatic component to suggestion, you don't have to go waving it around -- just hold it. Your DM might call for a check to palm the components or ready your arcane focus without being too obvious about it, but that depends entirely on the DM, the situation, and the nature of the tool you're using. Pulling a wand or orb out of your robes might be a lot more difficult to hide than using a staff you're always holding or leaning on, and if the item is already in hand it wouldn't necessarily be apparent that you're now using it rather than just holding it.
Best Answer
Spell Scrolls probably don't require any Components
As of the 2018 DMG Errata, the rules have gotten a bit hazier because of the particular wording of Spell Scrolls.
The wording now reads as such:
However, the section in the DMG on Magic Items still reads as follows:
So by a strict Rules-as-Written reading, the rules for Magic Items say "spells cast from items don't require components unless the item says so", and the rules for Spell Scrolls say "spells cast from a scroll do not require Material components", so we have to conclude that because Scrolls don't specifically say they do require Verbal or Somatic components, they must not require them.
However, I'm hard pressed to imagine a situation where Wizards of the Coast would make this change to the rules for a Spell Scroll if they expected that there would be no mechanical impact. It's possible they simply chose to include the extra line to make it clearer to the user what they're not required to provide (i.e. expensive Material Components) but it's also possible that they included this line because they wanted to retcon back in that scrolls do require Verbal/Somatic components, and simply chose a wording that doesn't quite manage it.
So while I believe the rules-as-written are quite clear, the rules-as-intended might be that spells cast from Spell Scrolls are supposed to require Verbal/Somatic Components.
A Spell Scroll might be Counterspell-able, despite this
Copied from my original answer
Simply because the action of grabbing a Spell Scroll and reading it will be visible to an enemy spellcaster, they may have the opportunity to attempt to Counterspell it, in a way that a regular Subtle-cast spell would only be Counterspell-able if it has Material Components. This will depend on the exact scenario where the Caster is casting from a scroll; if casting from a scroll that is already sitting in front of them, without clear evidence the caster is reading from it, the spell may not be Counterspell-able.