There are a few legal issues to consider. Anyone claiming that Trump would be committing an impeachable offense by issuing one of these pardons would have a difficult time making the case. The pardon is a constitutionally granted power. Could it, in principle, be used to obstruct justice? Sure, but when you have unclear rules versus clear constitutional powers, clear constitutional powers win out. Yes, Trump can pardon Flynn or Manafort. Would it obstruct justice in a philosophical sense? Yes, but making a legal case against that? That's hard. The Constitution wins.
Manafort has the possibility of state charges in New York, and Trump can't pardon him for those, but right now, so what? That doesn't give him a disincentive.
Then, there's the issue of 5th amendment protections. Supposedly, once pardoned, Manafort and Flynn lose their 5th amendment rights to refuse to testify, and could be forced to testify. Who's going to make them? Devin Nunes?
No, this really is on the table. For Trump, though, the question is need. Why bother? If he doesn't think that he'll be impeached or face criminal charges, then why bother doing anything politically dangerous, as pardoning Manafort or Flynn would be? Politically charged pardons tend to come at the end of a president's term. Arpaio was odd, but that was also a) a personal thing, and b) red meat for his base.
At this point, there are two questions: a) have Manafort or Flynn flipped, and b) will they flip?
If they have flipped, let 'em burn, for what few charges they have already faced. The question is whether or not they will flip. The pardon is a potential way to keep them from flipping, but what is the point at which they would flip?
What are the consequences of not flipping? Prison time? This is the kind of question Trump has to ask.
But, even if they do flip, so what? Congressional Republicans won't impeach, and a sitting president can't be charged with crimes without an impeachment first, so even if one or both flip, Trump has Devin Nunes, and by extension, Paul Ryan and the entire Republican congressional delegation backing him.
Prior to Nunes and the GOP reaction to Nunes, Trump may have had more of a need to pardon his way out of this, but at this point, it probably doesn't matter what Mueller does. If Mueller gets too close, Trump can fire Rosenstein, replace Rosenstein with a flunky who fires Mueller, have his flunky replace Mueller with another flunky, and bury the investigation. At that point, Trump is safe.
If a president has the unconditional backing of his entire party, that president is above the law. Does the Constitution say that? No, but that's how it actually works. How do we know that? Are you paying attention?