Karna's prana consumption
Gilgamesh is not using hundreds of NPs. He's using the Gate of Babylon, just opening a portal, shooting a projectile and then retrieving it, it's actually very cost effective. The only weapons he can actually release their True Names are Ea and Enkidu.
Source from Fate Complete Material III, on Gilgamesh: Tactics

Gilgamesh battles by shooting the originals of all Noble Phantasms like bullets via Gate of Babylon. The tactic yields excellent destructive power to magic energy efficiency. Since every Noble Phantasm is a bullet, the real magical energy used is merely the activation cost of Gate of Babylon. Because he possesses the originals of all Noble Phantasms, he can assault the weakness of any Servants. As a result, Gilgamesh has the advantage over most of the Servants in combat.

Artoria doesn't even have a proper path with Shirou, she's using her own prana reserves to use her skills. So no, Shirou is not sustaining her Mana Bursts.
Karna's Mana Burst (Flame) is just very high-maintenance. Extremely powerful as well, the dude is a fucking demigod, easily Heracles tier, who also has terrible prana consumption, Illya is probably the only one who could sustain Karna, much like she did with Herc. This last bit is pure speculation.