lawfag here
dems once again reveal theimselves via projection on secret pardons (see below) i was interested in this and dug a bit and the short answer is YES the President can order that a pardon be kept secret.
HOWEVER - if an indictment is publicly unsealed/issued that is covered by the pardon then the defendant would be forced to produce the pardon as a complete defense but POOF the secret is out.
So there is no reason to believe that Stealth Jeff or Mr. Clean would hesitate to indict even if they knew or suspected a pardon as it would expose the whole dirty scheme - of course if they ALSO had new charges post pardon those would not be covered.
OK now out comes a TIME article dated 11/11/18 which spreads the fake news that TRUMP will issue secret pardons! coincidence? to top it off a DEMRAT congressman is proposing a bill to require the announcement of any such pardons - lawfag doubts very much if congress can do that under separation of powers and other execituve issues but there it is.
http://time.com/4933386/donald-trump-secret-pardon-law/