Note, this extra drain thing was originally an optional rule. My group still runs it as an option rule, because the mage ends up feeling useless otherwise.. You have to keep in mind that casting a manaball at say force 6, is 5 drain that they have to soak. Chances are they'll get 3-4 on average, which ends up dealing them damage for each one they cast. This can quickly add up. If they have to soak an extra 6 for getting 6 hits, then they're taking SEVEN stun for that one spell. They probably killed some thugs, yes. But they're also useless for the rest of the fight. Meanwhile, GI Joe may take a whole 2 shots (still just one IP, just like the mage) to bring down this group of low level street thugs, and all he had to do was use two bullets out of his clip. Higher end operative can dodge the bullets, but if that manaball got counterspelled successfully (as can happen against tough enemies), that mage just took seven damage to do nothing at all.
If your groups main problem is the fact that all the enemies are super hyped up on drugs, twitching constantly and dodging everything with like 7 reaction and 6 dodge, then the GM is throwing awful enemies at you, as your average ganger would get around 6-8 dice to dodge, compared to the 10+ the guy should be shooting with. If you're fighting street thugs, it shouldn't matter who takes them out, it'll be easy for any member of the team. It you're fighting higher end operatives, then there would be a mage there to counterspell, as well as fight your mage back. Yes, that manaball you threw at them really hurt, but it didn't kill them. Now that your mage dealt himself 7 damage, how well can he counterspell that stunball from the mage nobody saw earlier? In one IP you've knocked out your mage, as well as taking heavy hits on each of your team members. With only 1-2 damage done to your mage however, he'll be a lot better at counterspelling (will+counterspell from a starting runner should beat everything but the most elite of operatives), and he'll be able to actually take any of the damage that does go through without being instant KO'd.
As for your final question, anyone behind cover is not hit by the manaball, as they don't have line of sight on the person. SR4A 183: "Some spells target areas or points in space; in this case the caster must be able to see the center of the area affected. All visible targets within the area are affected; area spells can affect more than one target at a time"