I don't think it is, although I couldn't locate a definitive source for this information. IIRC, 1.99 is the supported ssh version from CiscoWorks' various components. ssh v2 was just added in IOS 12.3(4)T, released late 2003. (See http://www.cisco.com/en/US/customer/products/sw/iosswrel/ps5207/products_feature_guide09186a00802045dc.html)
It does take a while for the management pieces to catch up feature-wise with what one can do by direct interaction with the IOS, though at a year and a half later, it's about time this happened. The development of the new Ciscoworks release was ongoing through spring-fall 2004 so one would think they could have fit in the ssh v2 support. It was a major re-architecting so I might surmise that feature just didn't make the cut.
