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Clutter refers to the unwanted or uninteresting stuff you have to dispense with before getting to what you want.  On a Q&A site, that usually means low quality questions.  These questions clutter up the site so that when you look around for good questions the low quality ones get in the way and make the process less efficient and more annoying.

Clutter is also more than just in the way when you are looking for something good.  It degrades the apparent value of the whole site when someone is first looking around.  In that sense, it's not as much clutter as junk that lowers the average quality of whatever part of the site is investigated.

And no, good search doesn't really solve the problem.  The search algorithm can be distracted by clutter just like a human.  A search might identify 5 question out of 5000 that match your criteria, but several of those 5 could easily be clutter.

One thing we do to combat clutter is voting.  Clutter would usually be voted down, while good content is voted up.  Differentiating questions and answers by vote score does help.  However, sometimes we don't want something else making decisions for us about what we want to see.  Then clutter gets in the way again.