Three films is too many for her to not know, imo. To me it starts to make her character look bad if the secret's dragged out for too long. Besides, some of their best dynamics are when they're already a couple. I say let them establish their rivalry/banter in Film 1, let them start dating early on in Film 2 and let Lois figure out the truth by the end of that film, and then let them be a serious couple during Film 3.
While I wouldn't have a problem with your lay out in terms of her finding out, I ultimately think they could go three films without her knowing.
It really depends on how much focus they give the romance in each film and what role the romance plays as the overall part of the narrative.
If the romance is as big a role in the films as Superman 1 and 2, BvS, MOS, or SR ,then , I would agree that revealing it only after 3 films would be too long.
But if the relationship, romance etc, is more of a smaller part of the overall story and the main focus is the threat, The overall plotline,other moving pieces , etc. I think they could put off Lois and Clark getting together and having a serious relationship.
Given that the audience knows they're going to end up together, and given they've seen them as a couple several times over the past 80 odd years, I actually don't think the filmmakers need to rush her knowing, and them being in a serious relationship.
Instead , I think they could go for the slowburn, assuming they pull it off well. It depends on what approach they want to go for and it depends on what the focus of the story is they want to tell.
If I were doing a few of Superman films, I'd actually go with the slowburn approach to the development of the rivalry, friendship , romance, triangle of Superman, Clark , and Lois as a secondary storyline through the films as opposed to it being the main driving force of the story.
I actually don't think it would make her look bad if she didn't know for a few films.
Audiences have pretty much gone with the idea that Clark's main disguise is a par of glasses, and that it fools everyone including his boss and Jimmy who are in constant contact with Clark and know what Superman looks like, and his arch nemesis and arch enemy , a master super villain who's in constant contact with Kent ,yet does all the research he can to on Superman.
The idea that the woman who loves him doesn't know ,or can't figure it out is a part of the myth, that audiences are willing to suspend their disbelief with.
I actually think it becomes more of a problem when its a "will they, won't they" Smallville like execution of the relationship or an "MJ and Peter" Sam Raimi Spiderman thing, and the dynamics those writers brought to the constant back and forth .
I can see why you would think that it would make Lois dumb, so I'm not dismissing your concern, but I actually think it wouldn't be a problem.
Then again, I have a pretty specific vision for how
I would do a series of Superman films and lay them out , so for purposes of my story, the main focus of the first films wouldn't be moving toward Lois Lane and Clark Kent becoming a couple. It's not the same way that Abrams or whoever may want to approach it.