Doesn’t hide all the empty rows based on the certain cell

When I saw both your Spreadsheet and your sample image, I thought that the values of "#REF!" and "" are required to be used. I think that the reason of your current issue might be due to this. So in your script, I think that it is required to add one more condition to the function shouldHideRow as follows.

Modified script:

function shouldHideRow(ss, rowIndex, rowValue) {
  if (rowValue == "" || rowValue == '#REF!') return true; // <--- Added
  if (rowValue != '') return false;

• By this modification, when the cell value is "#REF!" and "", sheet.hideRows(startRow + i) is run.