Hi Vincent,
Welcome to the forums and good luck with your LabVIEW endeavors!! You can indeed use MSDE 2000 with the Database Connectivity Toolset. The general rule is that any database that provides either an ODE DB Provider or an ODBC Driver can be used with the Database Connectivity Toolset. MSDE is fully compatible with SQL Server and uses the same ODBC Driver.
Hope this helps! Let us know if you have further questions,
Megan B.
National Instruments