Actually....
There's a few 3 & 4 player arcade cores and games on MiSTer - seven games outside of Capcom CPS1 & 2:
Gauntlet
Gauntlet II
Hyper Sports
Rampage
Snow Bros 2 (Toaplan)
Bullet (Sega System 16)
Dunk Shot (Sega System 16)
Captain Commando (CPS1)
Knights of the Round (CPS1)
King of Dragons (CPS1)
Final Fight Anniversary (CPS1)
Mercs (CPS1)
Muscle Bomber (CPS1)
Cadillacs & Dinosaurs (CPS1.5)
Saturday Night Slammasters (CPS1.5)
Warriors of Fate (CPS1.5)
Alien Vs Predator (CPS2)
Armored Warriors (CPS2)
Battle Circuit (CPS2)
Dungeons and Dragons - Shadows over Mistara (CPS2)
Dungeons and Dragons - Tower of Doom (CPS2)
Also, I think you meant CPS2 as a popular platform instead of CPS3. CPS3 doesn't have any 3-4 player games.
As it is with the current MiSTer hats (including MiSTercade), you can plug in two USB controllers for Player 3 and Player 4, or use a USB encoder (ie Undamned, Brook) to wire up your cab's Player 3 and Player 4 controllers.