Indeed, there is no problem with the ship
being incapable of warp in "BoT". But there's a huge problem with Romulans
being incapable of warp in "BoT", or even in the old war a century before the episode. And nowhere in the episode is it said that Romulans would lack the capacity - only that the ship would.
Nevertheless, it's a bold and dangerous claim from Scotty that their adversary can't do warp (if his words indeed denote this).
1) If he's capable of analyzing power emissions and therefore saying with confidence that the "simple impulse power" he detects is too little power for driving warp engines, then he's ignoring the fact that the ship has been firing very powerful weapons indeed; has been able to push those weapons to warp speed; and is using an invisibility technique Spock has speculated as requiring lots of power. He should
be thinking "Perhaps I'm not reading all
their power - perhaps I caught their reactor at a moment when it was throttled down".
2) If he's saying he can tell the enemy doesn't have warp engines in the first place, he's not just ignoring the very visible nacelles but also overlooking the sketchiness of evidence resulting from the ship being invisible for most of the time! He should be thinking "I don't know much about this ship yet, and while she hasn't directly demonstrated warp drive yet, I must keep looking for her warp engines".
He could be right, of course, in one sense or another, and this particular ship could be limited to sublight speeds due to her special mission just as you say. Only later events would show that this ship type is normally/otherwise capable of warp. But he's still too confident when he must
know that Romulans as a species are warp-capable and therefore were a threat in the 22nd century and remain a threat in the 23rd!