Here's my question: is this ever actually commented on, in setting? Does he realize he's magically super tough? Do people ever express incredulity that he could survive such a thing, etc? Because this to me sounds like plot armor out the ass rather than some sort of 'subtle' author indication of him being superhuman.
That's actually a rather tough question to answer. The author actually tries to have it both ways.
He can be supernaturally tough as per the incidents I mentioned in one scene and be perfectly vulnerable to mundane means (such as poisoning, being shot, etc.) in the next. In more lighthearted off-the-record books, the author through Touma jokes that he could actually be a clone or cyborg, though nothing in the actual series hints at either.
Later allies and antagonists postulate that Imagine Breaker itself possesses a will that helps Touma survive his encounters with higher-leveled espers and magicians even as it "nudges" him into those conflicts in the first place, but again, those theories are from the mouths of unreliable narrators and can thus be dismissed at least partially as bullshit. Touma's been in conflicts such as war zones and building sieges where Imagine Breaker would provide no benefit whatsoever, for example.
Given this author, though, I'd honestly say "plot armor" and call it a day.
In regards to your other question, what further complicates the matter is that, up until relatively recently, Touma has been notoriously incurious as to the nature of what he and his right hand actually are. For the first two dozen books, his attitude was explicitly that of regarding it merely as a tool to be used to protect what he felt he needed to protect. Lately, he's realized that he actually needs to know what's actually going on with Imagine Breaker as his enemies have started gunning for him and it directly, but given the tightly packed nature of the narrative, he's never been given the chance to actually find out the answers for himself without being fed bullshit by people trying to use him or being thrust headfirst into another crisis.