Don't be stupid for stupid's sake.
1. The terrorist's obviously wouldn't know the process of assembling a missile, or what that process looks like. If they did, they would have built the damn thing themselves. And I think it's obvious they had a hunch he wasn't building the Jericho, that's why Raza went in and interrogated Yensin.
2. Stane was not the PR guy. As explained in the movie, he ran the company after Howard Stark died, before Tony took the reins. It's like a President/CEO relationship. Obviously he didn't know how to make the Arc smaller. As stated in the movie, no breakthroughs had been made in the technology in 30 years, nor had resources been devoted to it since it was deemed fiscally unreasonable. The entire tone of that scene in Stark's office makes it pretty obvious that he thought Pepper was up to something. But you wouldn't want to just come out and accuse her of something, or esle she might become curious if she really wasn't doing anything.
3. I think the fact that they were in the middle of a crisis makes it all the more feasible that they wouldn't bother listening in on Rhodes' cell phone conversation. And, as I remember it, Rhodes never says outloud that it is Tony Stark in a suit. Tony tells him it is, but no one in the room would be able to hear what Tony was saying.
It seems to me like you need to pay more attention to what you are watching....