3 rounds of ammo is actually a buff, not a penalty.
In borderlands, there are several type of weapon components per weapon that alters stats such as spread, damage, reload, clip size, etc, but comes at a tradeoff of lowering another part of the weapon.
For the sniper rifle in particular, the component that reduces clip size to 3 also drastically improves damage. The trick is to offset this with skills, as Sorean suggested, or just use more sniper rifles, switch to other ones with the full clip. Hunters, who specialize in sniper rifles, can increase their clip size and reload speed, making them even deadlier with the sniper rifle. If you take a look at the component effects, you'll see that a lot of them boost one or two factors and take away from something else.
My favorite kind of sniper rifle in borderlands is the semi-automatic ones. Those typically come with a much larger clip size and firing rate at the cost of damage. The Orion, in particular, is awesome because its shot splits into three and ricochets, you can easily spam this at the feet of a group of enemies to take them all out.