I think this is off to a pretty good start. A couple of questions immediately spring to mind, though:
What kept the organisms from spreading in the first place? This thing was apparently around for thousands of years, yet it's still easily contained and not global already. Therefore it's either very geographically isolated with natural boundaries that hem everything in, or the creatures simply can't stray very far from the ark. Either option seems to make a physical wall unnecessary, particularly since the whole site could just be nuked if things got out of hand. Perhaps it's in a valley and receding glacier is the only thing keeping it bottled up?
As far as the spores, I'm no physicist, but I wouldn't bet my life on airborne fungicides being able to stop the spread of the spores on a windy day. I'd recommend enclosure in a dome, but this still leaves the question of why the spores weren't an issue in the preceding millennia. The SCP monitoring site would have to have heavy-duty filters of course.
Apart from the creatures, what's the rest of the biosphere of the location like? Has it been completely taken over? Also, apart from their weird shapes, how does the biology of the creatures compare to Earth's? As it stands, it doesn't seem like a Keter-level SCP, unless it shows the ability to aggressively transform the biome. As it's written, the barnacles don't seem inclined to spread from the boat, leaving them a local danger only.
Did they try to fly drones inside the structure?