, I think it's you that's been taking in too much terrorist fiction. The actual probabilities of the things you're talking about are so spectacularly small that they're not worth considering. The probability of someone, on this evidence, being the peaceable guy that Sai is, on the other hand, is enormous. By comparison to bomb parts, gigantic numbers of people have strange musical instruments or art pieces. Go ahead, research the numbers.
You say they gave him an opportunity to cooperate, but it doesn't sound that way to me. When you want to get information from someone, and you can see that they're willing and able to write, even keen to write, then you don't take pen and paper away from them. If you're truly seeking the truth, you let them write as much as they want. The reason to take that away from them is if you're afraid that what they write may harm or incriminate you. That seems to be precisely what happened: they were reminded that they were breaking the law, and they thought that the more they're reminded, the more culpable they'll be.
Could they have asked him to wait while they checked with their superiors? Sure. Could they have sent his stuff through the x-ray again? By all means. Could they have used the bomb-chemical tracer as they did? Certainly. But when they had the evidence that he did not have the means to kill lots of people, then whatever his intent, it was their duty to let him go. They didn't do that.
Try to think about an actual bomb plotter with a ceramic vessel and stuff that looks like old meds, and nothing on their person (verified by pat-down). You think they're going to opt out, for extra search? You think they're going to do anything but
smile and cooperate? Do you know how many actual weapons the TSA misses, because they look for "suspicious" people instead of doing their job? There are some interesting numbers on that, too.
Now, you have every right to your suspicions. The question is what you're suspicious of, and what you should do about it. If you're suspicious that Sai is not someone you'd like to have dinner with, not someone you'd like to lend your car to, or not someone you'd like your family members to marry, well, that's all your business. If, on the evidence of a ceramic vessel that you can see through, and evidence, at worst, that he's in a bad mood, you decide to be suspicious that he's trying to kill you and has a good shot at it, and then you decide to trample over his right to be safe in his personal effects and papers, well, then you're exaggerating the threat, and you've become a criminal.
That old cliché about those who are willing to sacrifice fundamental freedoms for a little extra safety? That applies to you right now. No amount of extra safety was even gained, because they already knew he didn't have bomb parts, from the x-ray and chemical tracers and pat-down.
The best way to protect the way of life we hold dear is to take seriously the liberties that form its core. The biggest threat to it is not terrorists, but people overreacting to terrorists with real terror, terror that leads them to give up their rights voluntarily. That (charitably) is what the TSA officers seem to have done here, and what you're in the process of doing. But it's not too late: you can, and should, reconsider.