It seems that no filter will be used when importing excel file. However, there is an X-Function, impExcel, which can be used to import an excel file. You can save the import settings as a theme file by using this X-Function. And then use this theme for importing your excel file in Origin C by calling this X-Function, such as:
LT_execute("impExcel fname:=D:\test.xls -t myImportExcel;"); // myImportExcel is the theme file name
You can try to see whether it can help.