If something in To Aru-verse can work to bypass Accelerator's defense in the way Dark Matter does... I think anything Shirou traces should do.
I mean, the traced stuff is literally from another world. That makes it considerably stranger then Dark Matter. Second, Noble Phantasms aren't just "awesome supernatural abilities or weapons", they have a sort of "metaphysical weight" due to their legend.
Being from another world isn't what messed with Accelerator; it was the fact that Dark Matter was Nonsensium and behaved in ways that made no sense, even to a guy that dealt with magic with no problem.
Shirou's stuuf may be from another world, but it's all made out of materials that come from Earth and make sense at least in a 'It's Magic, lol' way.
Also, from what read about Fragarach... it could kill Hecules once. Because it would work against God Hand--a defense.
Of course it could kill Berserker; it can bypass God Hand by virtue of it's A Rank. After that, it was an A Rank NP that scored a direct hit; of course he'd go down. Even then, it didn't counter God Hand; note how Berserker comes back afterwards. It just allowed for one hit.
The thing is, Vector Control works in a completely different way then God Hand.
So it's possible that for Fragarach, it would consider Accelerator's Vectors as his trump card, and counter them as a whole.
I think if Fragarach could kill Hercules once, it can kill Accelerator.
Once again, God Hand /= Vector Control. Besides which, Fragarach does not work like that. It doesn't flat out negate things; it goes shortly back in time and hits them before they can attack. If they die, which they usually do, it negates the attack.
However, as proven with Godhand, going back doesn't negate things that are basically always on (since Berserker comes back). It wouldn't work on Vector Control.
The question is if Shirou's seen Fragarach... does he have Shirou/Avenger's memories from Hollow Ataraxia? Did Shirouvenger see Bazett using Fragarach? Or was the Ur-Fragarach in the Gate of Babylon?
If he's seen it, then he can use it.
Dunno.
If he hasn't, though, there's probably something else he can use. And if there isn't, FATE!Shirou will take Archer's advice and imagine something that could do the job.
His powers do not work like that.
Let's hope Archer never came near Atlas and saw the Black Barrel or it's lesser replica.
Wouldn't really do anything due to how Black Barrel works. Accel's is a mortal, after all.
On a hilarious note, let's hope Archer never saw Shiki's knife: if he could download it's history of use, and if that replication momentarily gave him MEoDP, hilarity would truly ensue.?
Doesn't work like that. It would let him copy his skill with a knife, though, I guess.
Though, does this Shirou even HAVE Archer's memories?
Dunno.
And am I correct in thinking that the way Lancer's Gae Bolg was stopped was with Rho Aias? If so... Rho Aias is described as a "conceptual weapon that is said to be an absolute defense against any thrown weapon". It can block Enuma Elish and storms of swords. I think it can block vectors. While it's described as each layer being as strong as a fortress wall, it's more important to note it works as a Conceptual Weapon: that is, it works against ranged attacks by "saying LOLNO, that shit don't work, try again!"
Gae Bolg pierced Rho Aias and tore up Archer's arm (well, okay, it was about to pierce it completely, shocking Archer, so he dumped all his power into the final petal, but he still got hurt). Lancer was just pissed because it didn't kill him.
Also, while the Concept that made it a NP was 'block any thrown weapon (not projectile)', it's power is still 'seven fortresses'. As proven by Lancer, strong enough weapon can pierce it.
More importantly, Gil was almost surely holdng back because in...Heaven's Feel, I think, it takes Rho Aias plus Rider's Pegasus to survive Excalibur and Ea > Excalibur.
(Oh, and I guess I should note that Vector Control is a lot more versatile then that; he doesn't even have to go through it.)
If this Shirou has Archer's memories, then he probably is very, very good at using Rho Aias. And if he doesn't, he is still UBW Shirou, who used the full sevenfold shield. Furthermore, he has MORE circuits and can use them more efficiently, potentially. Which means he could use Rho Aias more easily.
Probably.
It wouldn't really matter, though, since Accelerator's powers include Multiple Exaton level explosions (i.e. the entire world's nuclear arsenal many, many times over and enough to destroy all life on earth). Granted, he would never use that attack to it's full power, cause he like the Earth how it is, but that's not the point; he can use any amount of power up to that point, at least (after all, he did that at half-power and wasn't tired afterwards; that's probably not his limit).
So, yeah, tl:dr version, Shirou has ways to attack or defend against Accelerator.
Not really...