I am trying to automate the BizTalk application deployment and achieved most of the task like host, host instance and handler creation using PowerShell scripts. But I have some JMS Adapters for which I need to update properties similar to shown in the below image. Is there any option by which I can automate the configuration of JMS Adapter properties?
While I can't verify the JNBridge Adapters fully support this (meaning you'll just have to try), yes.
You can follow this sample to set the Handler Properties: Set Send Handler Property (BizTalk Server Sample)
You will first have to export the Xml blob from this WMI Class: MSBTS_SendHandler.CustomCfg Property (WMI)