I used to use FindChangeByList but now I used Martinho De Gloria's Multi-Find Change. I know that It is able to run your queries on all open documents. It isn't free but it isn't expensive either.
//findType is "text", "grep", or "glyph" (this sets the type of find/change operation to use).
//findProperties is a properties record (as text) of the find preferences.
//changeProperties is a properties record (as text) of the change preferences.
//findChangeOptions is a properties record (as text) of the find/change options.
//description is a description of the find/change operation
//
//Very simple example:
//text {findWhat:"–"} {changeTo:"^_"} {includeFootnotes:true, includeMasterPages:true, includeHiddenLayers:true, wholeWord:false} Find all double dashes and replace with an em dash.
//
//More complex example:
//text {findWhat:"^9^9.^9^9″} {appliedCharacterStyle:"price"} {include footnotes:true, include master pages:true, include hidden layers:true, whole word:false} Find $10.00 to $99.99 and apply the character style "price".
//
//All InDesign search metacharacters are allowed in the "findWhat" and "changeTo" properties for findTextPreferences and changeTextPreferences.
//
//If you enter backslashes in the findWhat property of the findGrepPreferences object, they must be "escaped"