Depends on which silicone you are using. The Plat (food grade) series are a bit picky on what they cure against but The HS (High Strength) series are fairly easy going. What I would do is clean it with a hand sanitizing wipe instead of acetone and test a small mold using the HS series. The Amazing series (Mold Rubber and Putty) might also be fine after cleaning but if you're using steel masters then I'm guessing you might be doing several castings from the molds and sometimes it's better to use the HS series. Without knowing which silicone you are wanting to use, I'm just giving some general information that I hope helps you.
I would say that there shouldn't be any issues if the WD-40 is wiped off and the master piece to be cast is clean. With that being said, my main concern would be the HS picking up ANY left over residue that still may be present. If it where me I would test on a small area or part...if everything comes out O.K then I would say you are good to go.
Thanks for the responses. I am using HS-3. The outside surfaces are easy to wipe off but on some of the masters there are very tight faying surfaces. I am going to try a small mold on something similar and see how it goes.
I'm not sure what other "preservative" I could put on the items that would be ok. They are stored inside and not exposed to moisture. I may just clear coat the masters.