A native speaker who only just specified that there are exactly two agreements wouldn't use "all" to refer to them; he'd use "both". I.e.
Are these two agreements both right?
Are both these agreements right?
And even then, I'm not sure he'd use the word right in this case. Perhaps correct, or valid, or complete, or legal, or whatever suits the context — the point is, right is unlikely to be used because it would raise the question, right about what?
So for these reasons, "all right" quite obviously functions as a single unit here, meaning "fine, acceptable, adequate, satisfactory". There is no ambiguity.
But what if there were more than two agreements? Well, let's see:
Are these agreements all right?
This actually could be construed to be ambiguous; it could mean "are these agreements okay", and it could mean "are all of these agreements right". But again, in the latter case you'd probably use a different adjective and/or move the "all" to the front (like I just did). So syntactically both interpretations would make sense, but semantically the second one would still be more likely.