The reasons you often hear sound effects is because there's no way to avoid it sometimes in games. Just imagine you want a boss battle music and pausing the game mutes the music and there's no soundtest or music modifier cheat when you use an action replay. Then there's no way you can get the music by recording it. However OST's are different matter since they can often be higher quality because they're always encoded as 44,1khz instead of 32khz of 22,05khz plus they never have sound effects for the cutscene music(looks at Wind Waker).
There are ways to avoid them. For example, the battle theme in PM2 could be avoided by recording it from a Goomba battle with no first strike in Petal Meadows. Only effects you would hear would be the curtain rising.
Also if you are really serious about ripping game audio, you would take several recordings and edit them together to eliminate as many sound effects as possible.