sorry for the late reply, but actually it is possible to pass a search query without base64 encoding, i regularly use this to build urls in a "data assignment" step in workflow designer.
Here is an example:
This searches the fileCabinet for DOCUMENTNUMBER = "12345678" AND COMPANY = "MyCompanyName GmbH"
As you can see, the query is written in the same way as in a search dialog, you just need to escape the special characters.
Hope this helps.
Greetings from Germany,
Simon H. Hellmann
DocuWare System Consultant