What does hacking these consoles do

The Warframe wiki would suggest that completing a bonus objective will net you an additional 500 affinity. These bonus objectives appear to be assigned randomly at the beginning of a mission.

Relative to each other...:

The Afuris have a lower base damage (14), firing rate (20.0), and reload speed (2.7 s), but also have a greater magazine size (70 rounds). The Afuris would most likely benefit from damage, reload speed, and fire rate mods.

The Twin Vipers have a lower magazine size (28 rounds) and reload speed (1.9 s), but also have a higher base damage (16) and firing rate (25.0). The Twin Vipers would greatly benefit from magazine size mods and probably reload speed ones as well (to offset the reload times).

Both of these weapons have the same accuracy (8.7), max ammo capacity (210), and critical damage multiplier values (150%). Plus, as you stated, both have a terrible rate of ammunition efficiency. They do have some armor penetration issues though, so keep that in mind.

Overall, the Twin Vipers have a greater base max damage potential (3,360) compared to the Afuris (2,940). Yet, the Afuris have a greater base damage per magazine (980) compared to the Twin Vipers (448). You'll be burning through each magazine on the Vipers much faster, necessitating more reloads. Do you need sustained and quick (burst) damage? Go for the Afuris. If you need long-term damage, go for the Twin Vipers. Personally, I say choose the Twin Vipers but, make sure to slap on some magazine size and reload speed mods.