One main reason for a subsonic filter is that if we can't hear it and it's not needed for the music, it wastes a lot of amplifier power, makes the woofer do things that it wasn't designed for (like go to 10Hz) and since it's not part of the original signal, it's not helping the music. Most recordings are mixed for some nominal level of quality, not the best equipment. Look at what sells the most to find out what they're mixing for. In the early days, it was for radio, then it was for decent (but not great) phonographs, then it was for decent but average car stereo and now it's for iPods and iTunes. None of these can reproduce the deepest bass, so they mix the music down using smaller speakers, like Yamaha NS-10 (they're in so many studios it's incredible). This means they'll never hear any sub-harmonic content unless they play it back on something that can play deep bass well. If they never do, they'll never hear it and not everything that's on the master is intended. A four string bass guitar has a low E string that's normally tuned to about 41Hz. If the strings are sharp or flat, the difference between that note and the same one played on another instrument (like a synthesizer), will produce the original note, plus the sum and difference, called 'beat frequency'. The closer they are to being "in tune", the lower the beat frequency will be. If they're 12 Hz apart, you suddenly have a 12Hz note trying to go through your system and speakers. If they're 3 Hz apart, you now have a 3Hz note. This is the reason older stereos had a low filter- warped records produce these same frequencies and cause the woofers to flap around or bottom out and can cause feedback. It's also why a pilot needs to make sure the props are spinning at the right speeds- if they hit the resonant frequency of the plane, it will shake apart and suffer structural failure.
What the subsonic filter did is remove frequencies that weren't audible and were causing the speakers to modulate whatever came through that was audible. If main speakers are run full-range and a sub is used in the system, the mains should have the sub-sonics filtered out. If the sub is vented, it should have this, too- frequencies below the port tuning are poorly damped and can cause the woofer to become completely uncontrolled. This isn't quite as bad when the woofers are in sealed enclosures because they don't go to the subsonic frequencies very well unless they're aided, electronically.