It is unknown why a baryon sweep does not eradicate a starship itself, in view of the fact that all but less than one part in a thousand of normal matter consists of baryons.
A baryon sweep has also been suggested as a method to capture vessels without harm to friendly personnel. This could be done if the ship could be crippled, but the problem would be crippling the ship. It also seems quite a brutal method, but would probably secure a surrender very, very quickly. Repairing the rather insubstantial ship afterwards would seem to be a problem with this strategy for even the most ruthless races.