> but sqlite should be there, as it is being used in the system (if I am correct, at least by pkg, the new package manager).

AFAIK, no. PKGNG is intentionally not part of base, it's meant to always remain in ports. The reason is that it allows pkg developers to iterate quickly (and this ties nicely into the recent ports infrastructure overhaul efforts). Once something is part of base and goes into a RELEASE it pretty much has to stay frozen apart for security fixes, and this was deemed not flexible enough for pkg. The only thing in base is a shim pkg which on first invocation installs the real thing from ports (and, I think, later just routes everything to it, unless you remove it or change PATH). So nothing in base uses sqlite and it's in ports/packages.