Is it possible that logon.txt file in below command be encrypted using ccrypt function in linux and how can we use that encrypted file in bteq for example.
.run file logon.txt
The short answer is no. A file input to .RUN must be plain text. If you must use ccrypt, you could wrap the BTEQ in a shell script that unencrypts the logon command and redirects it to BTEQ's STDIN followed by the rest of the BTEQ commands (either inline or using .RUN for the unencrypted part).
Also check out the "Teradata Wallet" functionality to see if that will satisfy your requirements.