The Google Visualization API is limited to 500 results from a FusionTable.
Use the FusionTables v1 API instead, it does not have that restriction.
working version of your code:
<script src="https://www.googleapis.com/fusiontables/v1/query?sql=SELECT%20'FB_INDO_2000'%20FROM%201E9BosnI16GISRmTBkINI2aWlYVdZae46v8jClAc%20GROUP%20BY%20'FB_INDO_2000'&callback=drawMap&key=AIzaSyCAI2GoGWfLBvgygLKQp5suUk3RCG7r_ME" type="text/javascript" ></script>
function drawMap(response) {
var numRows = response.rows.length;
// Create the list of results for display of autocomplete.
var results = [];
for (var i = 0; i < numRows; i++) {
results.push(response.rows[i][0]);
}
// Use the results to create the autocomplete options.
$('#store').autocomplete({
source: results,
minLength: 2
});
};