The series runs on a comic book multiverse.
Think about it: as with DC and Marvel with multiple universes to account for different renditions of their characters, there are actually multiple Annies and Dick Tracys amongst other Tribune comic-strip characters. Harold Gray's universe is one, so do the later renditions until 2010. The theatrical/cinematic universe is also much different — the 1982, 1999 and 2014 Annies, not to mention the 1930s films exist in their own respective canons. Oliver Warbucks is one of Dr. Ort-Meyer's clones.
Well, both Agent 47 and Oliver are bald, they both prefer expensive suits and have amassed a significant fortune. Perhaps Warbucks is a Series IV clone who, like 47, was just as capable, but decided to retire early after being somehow disenchanted with his murderous lifestyle. He then set up an elaborate front as a successful businessman using the earnings from his contracts as a form of money laundering and lied to his adoptive daughter about his origins. Agent 47 IS Daddy Warbucks and Victoria is Annie.
Or in an alternate scenario, the plot of Hitman: Absolution is a twisted take on the Annie formula, i.e. a strong, imposing bald man vowing to take care of a young girl who has been through an unpleasant circumstance. Both Victoria and Annie had spent time in an orphanage, and both suffered from a cruel caretaker, Benjamin Travis for Victoria and Agatha Hannigan for Annie. Both girls were later rescued by similar-looking bald men who, despite being gruff and aloof at first, kept to their promise of giving them a better life away from abuse and exploitation—Benjamin conceived Victoria as a ruthless killer, much to 47's disgust, whilst Hannigan puts the girls under her (supposed) care to gruelling labour, to which Warbucks pledged to put a stop to.