function closeBooks() {
var books = app.books.everyItem().getElements();
var i, ilen = books.length;

for (i = 0; i < ilen; i++) {
    if (books[i].modified) {
        books[i].close(SaveOptions.ASK);
    }
}
alert('done');

}

if you call the closeBooks function, everything works fine.
But if the function is used as a handler, the "done" message appears immediately, before the for loop complete.

try adding a beforeQuit eventListener:
app.addEventListener('beforeQuit', closeBooks);

and close InDesign having one or more modified books to see this (strange) behaviour.

The same function works fine if you target documents.

InDesign CC2021 16.2.1 on MacOs Catalina 10.15.7