If Don Jr is charged with perjury, for lying about his dad’s involvement/knowledge of trump tower meeting (those mysterious phone calls) , then accepting a pardon means he is admitting his dad’s involvement
I think the bigger problem would be that Don Jr. could not use 5th amendment protections to shield himself from having to testify. For instance, say Don Jr. is under oath is asked about details of the acts for which he was pardoned. He would have to truthfully answer those questions, under oath and could not rely on the 5th amendment. Suppose someone asked, did DJT know of the meeting and true topics to be discussed at the famous NYC Tower meeting… Don Jr. would have to truthfully answer or face an additional perjury charge for which the pardon would not cover. Pardons can only be issued for crimes in the past, not the future.