LBJ did appear in Lois Lane #71, with a cover date of Jan. 1967 -- which would have put it on the stands in Sept or Oct 1966 -- and is addressed as "Mr President."
I do agree, however, that the assassination represents a major disconnect between Superman's world and our own. Having let Kennedy into that tight little circle of the "Superman Family," his death goes beyond merely "jarring" into flat-out irreconcilable. Things like that don't happen to Superman's friends.
For what it's worth, in this scene Lois is withholding from LBJ -- per Superman's wishes -- the fact that Superman has been turned into a cat (don't ask). So if nothing else, we've learned that the "if I can't trust the President, who can I trust?" rhetoric applied only to JFK, who in the world of Silver Age DC rises above his already lofty office to emerge as something of an honorary superhero in his own right.