Yes, There Was An Oracle in Rebirth
Yes, this fan-favorite graphic novel remains a "real" story, but it also establishes that the story's significant elements are firmly entrenched in the DC mythos. Moore and Bolland's story presented the origin of the Joker – or at least one of them, if the multiple Joker theory proves to be true – and has since become recognized as the character's definitive backstory. Perhaps more importantly, the horrible physical and emotional trauma inflicted by the Joker on Barbara Gordon also remains as part of her history.
Of course, this means that her time as Oracle has also survived into Rebirth. Barbara Gordon's reintroduction in DC's "New 52" in 2011 reestablished her as Batgirl, but called into question The Killing Joke's standing as canon. DC's editors assured its place in continuity, but her transition back to Batgirl largely went unexplained, and remains so well into Rebirth. Whatever the nature of her recovery proves to be, Doomsday Clock shows, not tells, that the circumstance of her injuries remains in place. Her resumption of her role as Batgirl, though, stands to be one of the many stories yet to be told in Rebirth.
It Was the Darkest of Times
If there is any acknowledgment of The Killing Joke on a more visceral level, it's one that speaks to changing mood of comics at the time. Watchmen was a dark examination of the superhero mythos that saw publication at the dawn of the so-called grim 'n gritty era. The even darker and more exploitive Killing Joke further explored a shadowy take on a classic hero vs. villain dichotomy. The amusement park reference is akin to an extension of the darker theme – Doomsday Clock not only continues the same vibe established in Watchmen, but also harkens back to the tone of the era in which Moore and Gibbons' seminal classic was initially published.
Eventually, the backlash against the ever-growing tide of darker and grimmer comics created a shift towards other gimmicks intended to grow readership. With a tale that takes place only seven years after Watchmen, though, Doomsday Clock reads like a straight-line extrapolation of where comic stories were heading 30 years ago. The reference to The Killing Joke serves in that regard serves as a marker, staking a spot in the mindset of which the story is anchored.
Doomsday Clock #2 shows that the series might hold a larger role than merely explaining the relationship between Watchmen and the DCU. Rebirth has shown that elements of DC continuity thought to be gone might just stand to return, but which ones remain might need further explanation elsewhere. Where Killing Joke fits has now been touched on, but plenty of other past stories might stand to benefit from a similar nod.