At some point during this presidency I went digging into it, and the legal experts I had found were saying that even though the pardon can be issued, if the person hasn't been charged then there are no double-jeopardy protections in place. Further, there was a supreme court case that stated that acceptance of a pardon is an admission of guilt, and suggestions that it could be used as evidence in a hypothetical trial. The conclusion was that even though crimes without charges have been pardoned before, that only works if prosecutors let it, not because it necessarily has to.

I'm not a legal expert though, and I don't know if that's the standard opinion, so I could be off.