You might like to think that but it will have an impact on the PK, d-zone faceoffs and the fact that Kennedy is horrible anywhere outside of the offensive zone.
A good coach should be able to take advantage of a defensively suspect Sheppard/Gomez/Kennedy (if that's what it is) line.
Havlat doesn't PK or take D zone faceoffs either, so they're gonna have those problems regardless. Moreover the Sharks have a ton of other guys who can PK and take faceoffs, including one on Burish's line who's just as good at it, so it's a negligible difference. As for the fourth line, I would guess that Sheppard and Gomez are two of the better fourth line possession players in the league, so I'm not that concerned about it. And no matter what the situation, you want your fourth line against the other team's top scoring lines as little as possible, so matchups will always be a concern.