Per-pixel collision detection is a pretty intense thing. Once you have thousands of objects to test, it can take a lot of time to check every pixel.
Don't worry about it, though - in practice it's not often you'll encounter problems with it, and as you said there are ways around it. I have a demo of a shooter where there were about 500 objects on screen and collision checks between almost all of them and it ran fine on a pentium 3.