You are allowed to have multiple versions of DX on your computer, as not all games use the same version. Crysis installed DX10 because that's what it uses. Other games, such as Resident Evil 5, you are given the option between DX9 and DX10. Or, newer games of which can run DX11. Each version offers difference amounts of quality in graphics as well as performance.
To answer your question, you shouldn't experience any performance issues from having multiple versions of DX, as only one version can be used for any given game at any given time.