Kraid has 15 missiles, or 3 Super Missiles, worth of health.
In a 100% run you'll be fighting Kraid with only regular missiles. You have time to get about 8 or 9 missiles into him before he closes his mouth, and the rest of the missiles to finish him off in the second round for an optimal fight. It's faster to fire two missiles per jump, one on the way up and one on the way down, but it's still possible to two-round Kraid with one missile per jump.
You should be entering this fight with at least 3 Super Missiles. As soon as the room loads you fire all three while running towards him and he's already dead. If you're firing too slow or you want to play it safe, you can fire the first two and jump to fire the third to make sure it goes in his mouth.
The only way to farm missiles during this fight is from the toenails he throws at you. After you deal 11 missiles worth of damage Kraid will turn red and destroy the platform you're standing on, which means you have to wait for his stomach platforms to shoot against the wall and that's pretty slow. For this reason an optimal fight is to count your shots and only deal 10 missiles worth of damage to Kraid, farm back up to your maximum 5 missiles, and shoot his face after he throws another volley of toenails at you. This should set you up with 4 missiles to fire into his mouth with 2 or 4 more missiles you can pick up to finish him off before he has time to enrage and destroy the platform.