LIQL - How to exclude message from board which has setting "Hide messages in this board from lists"

Hi pradeepc  You are right. It's showing the messages from those boards even setting "Hide messages in this board from lists" is applied. Might be it's an issue on lithium side. You can raise a to confirm it. 
If you want to exclude the messages from some specific and known boards than you can use the custom approach as well. 

<#assign excIds = ["Id1", "Id2","Id3"] />  //boards ids from which messages need to be excluded
<#assign msgs= rest( "2.0", "/search?q=" + "select * from messages order by post_time desc"?url).data />
<#list msgs.items as msg>
<#if excIds?seq_index_of(msg.board.id)== -1 >
//do something here
</#if>
</#list>