Maybe this hasn't come across, but Clark doesn't actually believe the story he's been told by Superman. This isn't to say he thinks Superman is lying, he just does not believe that Lois will ever learn to love him and thus doesn't see how their future could be the one that Superman painted. (Of course, you may agree with this.)
You're right - he is still keeping the true nature of his heritage from her, but this is much smaller than the fact that he moonlights in tights. Basically, he is not living a dual life here and so can be freer to be Clark.
This is just a hypothesis (but again, as the author it sort of counts for more than one vote) that part of what kept Lois from being with Clark so long in the show was the feeling that he was keeping something from her. Obviously, this at some point manifested itself in him making excuses and running off whenever she wanted to talk about their relationship, but the foundations for that had been set from the beginning. This Clark can be more open with her - he may be keeping his alien heritage from her, but no one is 100% open with someone when they meet. That takes time, for a relationship to develop, and so Clark wouldn't seem (in my mind) to be holding back any more than you would expect.
Still, this doesn't negate the fact that this Clark is missing part of his relationship with Lois by not being Superman and perhaps even more importantly, someone else is having those moments, making those memories, with her.
