CDs offer no way to check if the data copied off them is correct, i.e. there is no checksum stored on the disc that you could compare with to see if your files match those on the disc. The best that can be done is to rip it multiple times to make sure that the output is reproducible and this is basically what EAC does.
EAC (in secure mode) reads each sector at least twice. And if the first two reads don't match it continues reading the same sector in sets of 16 until 8 out of 16 reads produce matching outputs, up to a maximum of 1, 3, or 5 sets depending on your settings. This means that if you do a secure mode rip with test & copy in EAC, and in your log file the "Test CRC" and the "Copy CRC" are the same value, the data has been read 4 times from the disc with matching outputs.
But, obviously just comparing against yourself isn't ideal, which is where the AccurateRip and CUETools databases, containing checksums of rips by many EAC users come in. I've found that the CUETools database has often got discs that aren't on AccurateRip (especially with newer releases), so you might want to use the CUETools plugin with EAC if you already aren't. (When installing EAC, it'll ask whether you also want to install the CUETools plugin.)
The standalone CUETools program can also verify already ripped files against AccurateRip and CUETools databases. You can download it here:
http://cue.tools/wiki/CUETools
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After checking the WAVs it appears that some of them were empty.
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The only time I've had this happen to me is when I accidentally disconnected the CD drive in the middle of extraction (I use an external CD drive). If I remember correctly, in such cases EAC reports a lot of "Timing errors" in the log and impossibly high extraction speeds, so that could be a sign that something is wrong.