@Rozoro Look, I get that you may not believe that it would have a negative impact on their work,
but they clearly do. With that in mind, can you see why they might want to keep it a secret? Even if you don't agree with someone's reasons in taking a course of action, that doesn't mean that they don't have them. Is it so difficult to accept that some people might treat their work-life balance differently than you do? I understand that it's not how you feel-- but do you really think that no one has ever felt this way before? And then accordingly kept their relationship a secret? I mean, I'm not saying this is a completely realistic manga. Clearly, much, probably most, maybe all, of the reason for the secrecy is to entertain us, the readers. But is it really that unreasonable for someone to think that their work could be affected if their company and coworkers were aware of the relationship?
I used way too many question marks there. Anyway, let me try again with fewer questions. I can see why you could think they're being unnecessarily secretive. However, you said you couldn't rationalize it, which I took to mean "see the reasoning behind it at all". The reasoning seems quite clear as long as you accept the premise that they believe it would have a negative impact on work. So really, that seems to be the root of your issue with this. And if you truly can't see how someone might believe that, then that's that, I guess.
As for your last paragraph: eh, they'll cross that bridge if/when they come to it. Life is spicy sometimes.
Edit: Response to your edit (bridge with no sturdy foundations): They look pretty sturdy to me. Their communication is pretty good in general. They're head over heels for each other. They each care about the other's feelings. They seem to understand a relationship is a two-way street. Plus, being in a relationship isn't the only way to reject someone.
Edit 2, regarding all your doomsday scenarios: You're assuming they would keep this secret no matter what. People change their minds all the time. They could easily talk it over and decide to come clean with everyone at a later point, especially if they're having a freaking kid together. And if a serious accident happens, in many areas you aren't allowed in if you're not family anyway, so they'd have to be married. Pretty sure it wouldn't be a secret at that point.
Edit 3: And wait, how would this change anything if your partner was a devious asshole?