Wing Commander 2 was the last (?) game where tankers are evident. They are also the last game without evident ramscoops on the majority of the ships (the Gilgamesh has some over-wing ports with red dots that seem similar). I know from fiction (End Run, Fleet Action) that ramscoops were common prior to the battle of Earth and were equipped on small patrol craft such as Ferrets. Do we know if there is a (deliberate) correlation between the lack of tankers and the visible ramscoops, and what the purpose of a tanker would be if even small craft could scavenge their own fuel?
You get a ramscoop! You get a ramscoop! Everybody gets a ramscoop! (Every Wing Commander ship has a ramscoop.)
Short answer: no, no correlation between the rise in references to ramscoops and the decline in tankers. The ramscoops are actually an Origin concept... and there are plenty of tankers in later games and stories!
I believe the ramscoop idea first appeared in the 1991 licensing bible, which is why it's so prevalent in the novels. It was the handwavium that Origin came up with circa Wing Commander 2 to explain how the ships work... and writers like Dr. Forstchen who had never played the game assumed it was a big part of the lore.
The concept is that the ramscoops slowly take in hydrogen which allows the ships to maintain their cruising speeds like a real aircraft (versus real spacecraft, which carry a few seconds worth of fuel and mostly travel based on momentum and orbital mechanics)... which is what you see in the games.
Faster speeds (especially afterburners) burn down your fuel much more quickly than the ramscoops can hope to replenish your tanks. Then the other thing that burns fuel quickly is jumping. It's not a coincidence that the tankers we 'interact' with in Wing Commander II and Prophecy are there to replenish fuel used during jumps and afterburners, respectively.
As we see in Action Stations, a ship that runs out of fuel is essentially screwed--it needs to idle for days/weeks/months to scoop in enough hydrogen to fly anywhere again. (Note also that regular flying isn't a 1:1 thing... in continuity you do eventually run out of fuel. It's just a way to make the spacecraft behave more like fighter planes.)
What you're seeing with the clear 'intakes' in Wing Commander III forward is a conscious attempt on the part of the designers to have a unified design for the ships, per Chris Roberts' edict that the designs be more "realistic".
WC3 also has tankers (the Torgo Behemoth series). I don't recall any tankers in WC4 (hopefully my memory is working since I just replayed it this weekend).
No tankers in WC4, although you are specifically ordered to land between attacks on the Vesuvius for refueling. And Peleus is "a major source of fuel".
Also relevant to the original question--tankers actually show up in every single Baen novel (and Pilgrim Truth).