Is any way how to find you whether some node exists in web config? SPWebConfigModification? or some other class? I belive there must be way how to find it out.
The SPWebConfigModification, as you may already be aware, is used purely to make changes to the web.config in SharePoint which can then be propagated across a farm.
To check for the existence of a section you may be able to use the WebConfigurationManager from the System.Web.Configuration namespace (System.Web assembly) - see http://msdn.microsoft.com/en-us/library/system.web.configuration.webconfigurationmanager(v=vs.90).aspx.
Hope this helps.