Does ZU.13 Key Master confuse the MU rule?
The reason for the "even if it is not installed" language is to allow you to install ZU.13 Key Master even if you are already at your MU limit. You are of course correct that cards in your grip do not count against your MU limit.

To explain formally: p. 6 of the rulebook states:


  Cards in the grip are inactive


and from p. 4:


  An inactive card’s abilities do not affect the game


So without that phrase, ZU.13's ability to not cost MU would not work until it was already in play, and if you were at your MU limit, you would still have to trash some other installed program before you installed it. With that phrase, the card's intent is achieved, which is that it "costs" 0 MU as long as you have at least 2 link strength.