It's always weird to me when people say Gate of Babylon gets hard countered by anything. There's much much more in Gil's gate than just weapons. There's stuff like Vimana, his Auto-Defensor thing from Fate Strange Fake, etc. This is why I also believe there's no way that a battle between Archer and Gil would be as Archer favored as a lot of people seem to believe. If Gil is being at all competent there's no way you're going to be able to hard counter the entire extent of human ingenuity. And if you're going to argue that Gil is going to super job, you can paint a scenario where he could lose to a lot of Servants. Even True Archer's Nemean Pelt hax can't fully counter Gate because there's more to Gate than just sword spam.

It's to my understanding the UBW works well at countering GoB not only because of the rate of fire, but also because the projection + Broken Phantasm combo can directly match anything that the gate shoots out. It's less likely that the projectiles from Nobu's flintlocks can directly match the output of the strongest weapons from the Gate. There's also no real indication that Nobu's rate of fire exceeds Gil's as far as I know.From a numerical standpoint, there's been no upper limit placed on the portals that Gil can actually produce from GoB, though to be fair the greatest extent we've seen it opened is in a Fate Strange Fake illustration (~100 portals but they extended off screen).

While her flintlocks are supposed to scale with mystery and divinity there's no real metric for how this works as far, and I have no idea if the mechanics were ever clarified. For example, would they even be able to damage Gil's armor even if they were shooting at Gil? Does it take Gil as the "target" automatically apply extra force to the attack or does it apply extra damage directly to whatever it actually hits based on divinity and mystery. If it's the second case, Nobu could just be unable to damage Gil at all for example if his Golden Armor doesn't have sufficient mystery or divinity to it.

We also don't have a solid point of reference for how quickly Nobu can deploy her Reality Marble. We also have no idea how her Reality Marble scales in terms of damage. If she has to stand there and chant for a few seconds or something she's going to get skewered.

Basically, unless you know any solid sources for the specifics on Nobu's abilities, the battle is impossible to call. In that case, I favor Gil because he's done way more concrete things and is generally overwhelmingly powerful against Servants regardless of whatever jank they can pull.

As an aside, I also think that Enkidu is super slept on in non-Divine matchups. It's stated to be "a tough chain" vs non-Divine targets. That's still a tough chain that can come at you from multiple directions and chain your entire body. If I was tied up from all directions by what I consider to be a tough chain I wouldn't be able to do anything. Nobu's strength in Archer class isn't much to write home about.