Why are Excavata called "Excavata"?
This is just a reference to the feeding groove - a morphological feature that groups these organisms. The presence of the term in quotes as "excavated" is an indication that the word is not meant to be taken literally. Quotation marks used like this are referred to as scare quotes - they are meant to alert the reader that the phrase in quotes is not to be interpreted by its standard meaning.

Instead, you could read the sentence as meaning:


  Some members of this diverse group also have a feeding groove on one side of the cell body, as if part of the cell was excavated.


One should not take the etymology of species names too literally - they are really just names. This is also true of common names of organisms.