Instruments are "two handed" in the secondary slot. You cannot duel wield and equip an instrument. The lone exception to this rule (in Kunark) is
Ervaj's Flute of Flight, the Bard Sky quest flute which is Primary only and will allow you to equip a weapon in Secondary.
Also a note about the Singing Short Sword (epic): you must equip the epic in your primary to receive the instrument/singing bonus (1.8x mod). This is changed in Oct 2001, 2 months before the release of Luclin. So get friendly with your SSS, you'll be using it for a long time to come (
bug report).