Don't forget what happened afterward. Sure, in the Lester version, Lois was completely fooled when Clark didn't turn into Superman to save her at Niagara falls. But in the Donner version, the one we're talking about, the one where she jumped out the window, she wasn't fooled for long. She may have failed to prove Clark was Superman, but she still suspected that he was, and in the great scene that unfortunately was only ever filmed in the actors' auditions (footage of which was incorporated into the Donner Cut), she forced Clark to reveal himself by shooting him (with blanks, which he really should've noticed).
Ah! Okay, I'm clearer on what we're talking about, I recall those events in the Donner version.
And, yeah, Clark should have noticed he was shot-at with blanks, given that nothing would have hit him. Though maybe even if the gun had
been filled with bullets he wouldn't have felt them as the impact they'd cause are too well below his threshold of feeling them. It'd be like a human getting "shot" with a speck of dust. We're so much more powerful and stronger in comparison it's not enough to notice it.
So Lois fires the blanks and Superman says, "Oh shit! She's shooting me! I don't normally feel bullets... Uh... act shot!"