Wow.
Another BB JDE surprise
I met the problem either.
Looks like there is no way of simply doing this. JDE calls rapc.exe which is wrapper tool for javac. I didn't find a way to define params to rapc.exe within JDE.
What I did:
You can copy the command line from Build Output window (the one with rapc.exe), open command line window, go to dir where your project is located, paste the command line, add -deprecation as the rapc.exe param.
Worked for me.
Wojtek