Subsonic filter explanation

Usually it's used to make the amp more efficient.  By that I mean that it only allows the amp to reproduce sound which you will actually be able to hear.  Therefore, if the music contains sound that would still be inaudible even if you had speakers that could reproduce it, an amp with a subsonic filter will be able to concentrate all its power into reproducing meaningful frequencies.

I've never actually done side by side comparisons to see if it really does make an amp more efficient in the real world, and of course this would also depend on what kind of music you listen to, and how good of a CD player you have.

Also it should be noted that many head units, amps, processors, etc. do not even reproduce/amplify these subsonic frequencies.  In this instance a subsonic filter would be essentially useless and its effect on the amplifier's efficiency would be minimal.

In the situations where you have very high end components that ARE capable of reproducing these subsonic frequencies, a subsonic filter will also serve to protect a speaker from damage due to over excursion.

In general I wouldn't really pick a certain amp over another one simply because it has a subsonic filter.  as I said before the applications of these are usually limited to very high end systems and the average user won't be able to tell much of a difference.  So to answer your question about disadvantages of using an amp w/o  a subsonic filter--there aren't really any in most situations.   Now obviously if you're talking about competition systems, where every single watt needs to be used most efficiently, then subsonic filters may actually make an audible difference.

One more thing to add-- a lot of manufacturers define a "subsonic filter" differently.  For example, some companies have their subsonic filters cutoff frequencies at like 40 Hz which in my opinion is way too high for a sub.  Others keep it at 20 Hz which is a much better frequency as this is the limit of human hearing.  I have also seen a couple of them that are adjustable.  Just something else to keep in mind.