Oh, are they hooked up to the "GUN" inputs? I figured those were actually, you know, light guns 
The
buttons wire to the "Gun" inputs in the "gauntlet" 49-way mode. The 49-way joysticks (8 pins ) go where the 8-way joystick & buttons would go if in 8-way mode. FWIW, for player's 1&2, that's jamma's 8-way joystick and four (neogeo) buttons pins.
IIRC, for the sports games, all 49-way joystick data goes to player 4's four (8-way) joystick pins, multiplex'ed at 8x the normal input (twice since each axis uses 4 pins, for the two axes, multiplied by 4 for the players). Talk about over engineered.
If those can be used as GPIO, then that gives them all the inputs they need. Blitz would likely only use an I-40 for backwards compatibility with Seattle, then.
Compatibility would make sense I guess. But as I said,
all the midway sports games need the I-40 regardless if vegas (NBA Showtime, Sportstation, Blitz 2000 Gold Edition) or seattle (Blitz, B99, B2000), while both the 3D gauntlet games don't, again regardless if vegas (dark legacy) or seattle (legends). As you can see, Gauntlet Legends is seattle based, and didn't use I-40.
I think it's a Midway vs Atari thing. NBA Showtime included two games, one being Blitz 2000. So B2000 is on both seattle and vegas boards (I'm not sure on the amount of recoding done between the two, though). And even though DL was released as a "Midway" game, it was written by the same studio as Legends (California based, "Atari Games" renamed to "Midway Games West"), while the sports games were written by the main Midway studio (Chicago based). So IMO, DL is really an Atari game, running on "Atari Vegas" boards.