I'm one of the old school and love all the secret identity shenanigans of comic books but I can understand why they abandoned it here. We all know she finds out anyway and it has been done to death so may as well take the road less traveled.
Yeah I definitely see the appeal, and the previous comic and live-action versions of the character had a lot of good fun with it. But in this day and age-- and especially in a serious movie like MOS-- it just seems a bit ridiculous to think that Lois wouldn't recognize him under the glasses (the others, maybe not, since they don't see Supes up close as often as she does).
But the good thing is there's still plenty of room for romantic tension in this idea, not to mention humor with Lois having to constantly pretend this Clark guy is just an everyday reporter. And I like the idea that they have this huge secret between them as well (which thankfully doesn't require them being married like in the comics).