First of all, why is this called the "Denabase" in the rulebook when in the movie "Blade Runner 2049" it's called the "DNA Archive"? This just strikes me as an odd and unnecessary change.
Just a guess on my part, but it's possible that 'DNA Archive' is the official name for this particular database, and 'Denabase' (DNABase) is the nickname used by Rep-Detect personnel on the job. Civilians might not even know what the term 'Denabase' refers to.
Page 188 says it contains records of "all registered LA civilians". I would say this excludes replicants as they are "product" rather than "civilians".
The fact that Nexus-9 Replicants can't be citizens is the reason for frequent protests by Sympathizers. Judging from that, it's likely that only the Wallace Corp's files hold any clue as to who is actually a Replicant and who isn't. Of course, there's Rachel Tyrell to consider... and it's possible she's not the only citizen who has had a Replicant copy running around off the books, past or present tense. Think about the fun you can have with your players with that fact alone!