Vacuoles were named because when they were first seen they looked like empty regions in a cell. They're not actually empty, but appear to be a place where cells store things which dissolve in water. Large vacuoles are a normal feature of plant cells, but are not so commonly associated with animal cells.
Vacuoles in sperm are an indicator of poor(er) quality. A single small vacuole is probably OK.
Supposedly selecting sperm without vacuoles gets 55-60% of embys to blastocyst, while having large or numerous sperm vacuoles only gets 0-5% to blast. http://www.ivfnewsdirect.com/?p=144
Now for my personal interpretation of the info. I suspect a sperm that's accumulating damage might try protecting itself by shoving nasties into a vacuole. Therefore large or more numerous vacuoles is an indicator that the sperm has suffered extensive damage and that the DNA is not likely to have been spared from the attack.