Actually, when Daniel meets Barnabas, he's pretty much out of it and lost in the past, [spoiler]saying something like, "You had us quite worried for a while, running off to England like that, and then we never heard from you." But Barnabas explains that Daniel has Barnabas "confused" with his father, which confuses Daniel all the more until Ben has to remind him that the year is now 1840. Considering the way Daniel behaves during this meeting (and just prior to it when he was confusing all sorts of other things from the past), it's actually a wonder that he remembers his own name, and no wonder that he doesn't remember that Barnabas is "the secret."
However, things are very different shortly thereafter when Daniel meets Valerie (in Ep #1131) and does recognize her as Angelique. He does indeed put things together, saying something like, "And Barnabas - if you have remained the same, has he?" But, of course, Angelique causes Daniel to forget his recognition of them for who they really are (revealing a shocking secret from Daniel's past in the process), and that's the end of that.[/spoiler]