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.
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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.