While you can't Zebra stripe a table with hidden rows using CSS3 you can do it with JavaScript. Here is how:
var table = document.getElementById("mytable");
var k = 0;
for (var j = 0, row; row = table.rows[j]; j++) {
if (!(row.style.display === "none")) {
if (k % 2) {
row.style.backgroundColor = "rgba(242,252,244,0.4)";
} else {
row.style.backgroundColor = "rgba(0,0,0,0.0)";
}
k++;
}
}