question

Here's a method using one sql statement (just these two lines are needed):

Table t=Table.query("SELECT SUM (Quantity* (CASE WHEN Size='S' THEN 0.2 WHEN Size='M' THEN 0.4  ELSE 0.6 END )) AS TotalPallets FROM GlobalWarehouseInv");
print (time(),"Total Pallets:", t[1][1]);

Here is your original code with corrected syntax which will print the same value to the output console:

double itemPallets;
double totalPallets;
int palletItem=1;
double numRows=List("GlobalWarehouseInv").entries().length;

while (palletItem<=numRows) {
    Table t=Table.query("SELECT Quantity, Temp, Size FROM GlobalWarehouseInv WHERE MatlName='Item "+palletItem+"'");
    double numItems=t[1][1];
    double temp=t[1][2];
    string size=t[1][3];
    
    if (size=="S")
        itemPallets=numItems*0.2;
    else if (size=="M")
        itemPallets=numItems*0.4;
    else
        itemPallets=numItems*0.6;
    
    totalPallets+=itemPallets;
    palletItem++;
}
print (time(),"Total Pallets:", totalPallets);

The first thing to note is using the list entries instead of table numRows.

The next is that the material name is enclosed in single apostrophes as it needs to evaluate as a string not a column name or variable.

Another is that you can get all three values for a record in one query.

In order to debug your code you can place breakpoints on one or more lines which will open the FlexScript debugger and allow you to inspect local variables and evaluate expressions using them. If that was the purpose of printing to a console then the debugger is going to be more powerful than print statements, although there are still some occasions where you can need both.