Tom Clancy was never involved with the games that bear his name. He was a political thriller writer who decided to become a brand: publishers simply wanted to leverage it in the late 90s/2000s, as a lot of Clancy stuff was popular in the mid-market segment. As for Meier, Micropose simply slapped his name on the cover of Pirates! as they wanted to capitalize on his reputation among flight sim enthusiasts. The early PC gaming scene was full of ripoffs, clones, etc., and this was their way of establishing their own identity.
Kojima's habit of putting his name on the cover began with MGS2: Substance - as his clout within Konami started to rise exponentially, ending with his promotion to EVP in 2011. I pretty much think it comes from his perennial frustration that he's a game designer and not a filmmaker. The "vanity credit", as it is known in Hollywood,
was never really popular with those in the production staff or with the writers, but became increasingly common as time wore on.
It's preposterous, really, since directing a game is not like being a filmmaker. You're most likely in an office, with a shitload of stickies on the wall, meeting with different leads who come to you with wireframes, mockups, ideas, etc. You'll realize Kojima, for example, always shares writing credits with someone else (Tomokazu Fukushima, etc.) - what that means is that Kojima here is not really putting pen to paper, but giving general directions, intimations of plot and character, for his co-writers to go ahead and draft.
Kojima, when at Konami, always had an assistant director - usually Yoshikazu Matsuhana. Let's look at what Matsuhana said about his role in an interview with a Japanese publication about 20 years ago (one can find transcripts online):
A filmmaker is on set, behind the cinematographer, directing shots, coaching actors, etc. A game director is an executive - he handles planning, keeps the Executive Producers and Steering Committee off the project's back, drafts design documents explaining his or her expectations, etc.
Some Japanese directors, like Yasumi Matsuno, are all about plot, setting and feel, leaving others to do the technical heavy lifting. Others, like Miyamoto, have their hands on everything. A third group, like Yuji Naka, is all about the technical aspects of the game, leaving the artists to do their thing. But they're usually not in the thick of it, and all of them rely on Leads, Assistant Directors, etc. etc. to carry out their bidding.