No, the webagents are backward and forward compatible. So, 9.0 webagents should be good with 9.0.00.01 SSO Server.
For the issues which were fixed as part of 9.0.00.01 you can refer the link here.
You dont need to re-run the integration again to upgrade the webagents. Simply copying the 9.0.00.01 jars to MT/AR would be enough.
Hope this helps.